I've always preferred trousers but I've been wearing jeans a lot lately. It's just the unfussiness of them that's difficult to replace.
In summer linen trousers win but I'm going to have to get a couple of new pairs made.
Id be more worried about getting fat over that time period than losing gains. Would use the time to do some dieting or something so that you stay motivated when you get back to the gym. If it fits in with your game plan.