i dont see how it can possibly pull the subframe out of alignment by replacing the arms. the only way the subframe is going to move is if the subframe bolts are lose. is the subframe mounted with bushes or is it solid like on the focus??

when changing one arm i would always change both at the same time to minimise any differences in size and then get the wheel alignment checked and adjusted (made the mistake of not doing that on an old escort and killed the tyres ). if you tell them its had new arms most places will tell you to come back in a couple of weeks for a free check and adjust as they settle.