The Church of England's administrative headquarters in London has reinvented itself in recent years as a handy conference venue. You can see why; it's perfectly located in Westminster and the venture provides useful revenue. Nearby Methodist Central Hall (MCH) has done the same, and the income from events supports a thriving congregation there.

Money's always useful, but Mammon is an uneasy business partner, as MCH found when it hosted a UKIP conference to howls of outrage from left-leaning Methodists.

Now, Church House Conference Centre has become the target of groups protesting against its use for conferences sponsored by arms manufacturers including BAE Systems and Lockheed Martin. The conferences are the RUSI Land Warfare Conference, held a fortnight ago, and the the Chief of the Air Staff's Airpower Conference held earlier this week.

According to the protesters, who include representatives of the Fellowship of Reconciliation, Pax Christi, Campaign Against Arms Trade Christian Network, The Drones Campaign Network and Christians for Economic Justice, it's just wrong that the Church should be associated with this kind of thing, even at arms' length. By hosting such conferences the centre is, in the words of one campaigner, "sending a clear message that they are happy to profit from those selling weapons to the dodgiest regimes".

It's a powerful statement. But here's why I think it doesn't add up.

The protesters are pacifists, who believe that killing people in warfare is wrong. What Would Jesus Do? Not that, they say. That's fair enough: I don't know any Christian who believes that killing people is ever "right", in an absolute sense. The best that can be said for it is that it's sometimes necessary – though Christians should always question that necessity and be prepared to suck up a good deal more provocation, or temptation, before we assent to war. In that sense we're all pacifists.

But fundamentalist Christian pacifism is different. It wants the Church to declare its outright opposition to warfare and all its works. Any compromise is out of the question. Hence the opposition to the arms trade: guns kill people, so making guns in order to kill people is wrong, so the Church should have nothing to do with people who make guns. The military kill people, so having a conference on church premises for the military is just wrong. We need to keep our hands absolutely clean: the business of killing cannot be allowed to taint the pure spirituality of the Christian Church.

The problem is this. The Church of England, along with the other mainstream Churches, certainly has a problem with violence. I'm rather glad about that; I'd hate them to be all gung-ho and aggressive. Like other Churches, there's a pacifist witness within it. But the CofE doesn't believe in disbanding our armed forces and spending the money in less lethal ways, either. Like almost everyone, Christian or not, it sees that the world is a dangerous place. Whether our armed forces have been usely wisely in recent years is frankly moot – and yes, from a purely strategic point of view, there are serious questions about a Trident replacement or those two huge aircraft carriers without any aircraft. But would the world be a safer place if Britain didn't have a military? No.

I don't defend every war we've fought. Some of them have been stupid and wrong. That's not the fault of the army, but of the politicians who sent them to war. But I agree with the former Sandhurst commander Maj Gen Andrew Ritchie, who once said: "The Army is a moral force. It's a force for good in the world. That's why people join."

Here's the thing. If you have to have a military – even if it's smaller, less well equipped and less adventurous – you need weapons, and someone to make them. You need to think about what your military does and how to do it better. And if you believe that we need armed force to protect us, trying to detach the Church from all that isn't prophetic at all: it's hypocrisy.

Let me be clear: if the protesters at Church House this week genuinely believe that we don't need a military at all, I would respectfully disagree with them. I'd ask them what they'd have to say when violent men terrorise whole populations. If they say, fairly enough, that in some cases it was bad policies and unwise interventions that sparked the conflicts in the first place, I'd agree – while pointing out the numerous exceptions – and ask them how that was relevant, given that we are where we are.

I'd disagree, but I wouldn't impugn their integrity for one moment: these are people of high principle. (Having said that, their principles are no higher than those of people who take the contrary position. A declaration of non-violence does not absolve them from responsibility for the consequences in a violent world; non-violence that permits violence to be inflicted on others is morally questionable too.)

But if it's once admitted that we need a military and everything that goes with it, the Church cannot subscribe to the sort of gesture politics that refusing to hold these conferences implies. It cannot hold its hands up and say, "We're not involved." On the contrary: it should be intimately involved. It should not shrink from taking up the burden of making and shaping moral choices in this area as in every other.

The RUSI conference at Church House this week included an address on " Understanding the Motivations and Capabilities of Non‐State Actors" (ie terrorists) by Air Commodore Sean Corbett. The previous one included consideration of "New Ways of Warfare" dealing with the information age and "military activities short of war".

I'm glad people are thinking about this stuff, and I'm glad it's happening at Church House. I'm glad that the Church isn't trying to wash its hands of the messiness and inevitable compromises involved in being in the world.

I don't like war, and anyone who says they do is a wicked fool. But I don't believe that Christians should be trying to distance themselves from anything to do with war just because it's wrong.

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