The point is fairly academic, given that if we're pulling civilian(ish) yards for military purposes, we have a war and in turn SoE to do so. This negates political concerns. Similarly, I would expect that a full-out shooting war that was tapping our resources to the point of needing those yards would result in secondment of equipment to the yards to do the work prior to needing them. And while said yards might be less secure, wartime measures would likely result in sufficient security that, if the need was dire enough, we'd end up using them regardless. Since, really, if things are bad enough that all of Starfleet's yards and all the member/affiliate yards are in use, then things are bad enough we will be scrambling for any berths we can have. Security and efficiency pale in comparison to sufficient need.