Morghast, I completely get where you are coming from.
My wife and I started the game together about 3 years ago. We have always generally played together, leveled toons together, been guilded together, etc., although I play a lot more than she does so I have 8 85's while she has 3; I have sets of toons on multiple realms just to tinker with while she stays on our main realm.
A few months back a bunch of guild drama unfolded (wife was chatting over vent with somebody about alts and how her priest was really ungeared - guildy priest was raiding with us thought she meant her - guild leader *called* wife on phone few days later chewing her out for being mean) and my wife pulled all her toons out of the guild. This was around the same time Skyrim launched so I ended up wandering off to play that mostly, only showing up for raid nights with the wife and our non-guild raid crew. I didn't really talk to my guild much after that, although I'm still in it.
She is a really good tank and now geared in at least half BiS stuff, and has gotten multiple guild invites but is much happier just lone-wolfing it. I bored of Skyrim and am back to "full-time" WoWing and I find now there are a lot of times outside of raid nights that she goes off to farm mats or mog gear, and I'm off doing my own thing. I try to get my 6 LFR geared toons through a full LFR clear each week and am in the process of collecting desired mog gear for all of my toons as well as trying to level some horde toons on other servers.
I wasn't sure how it would all shake out but it's honestly working just fine. We still have raids together and I'll run an LFR with her one toon she actually uses but most of the rest of time we just do our own things. We're still sitting right next to each other. At our gear levels, neither of us really has much use for endless (or any, really) dungeon grinding so we just do what we each want for our toons. Everybody seems happy with it.
Our problem with the guild, really, is that while we're both really solid players, some of our crew was really, really terrible. It lead to a lot of frustration between us because we were doing everything right and wiping on the same bosses repeatedly week after week after week due to utter failure by others, and while I'm pretty non-confrontational, she has no problem spouting off. So our issue was "how do we deal with being surrounded by a mix of really awesome people and idiots?" Instead of your situation where you were stuck in the middle, I'm now sitting in a guild where nobody has said anything to me in weeks.
In a way, it's kind of freeing actually. With her gone, I have zero interest in, or loyalty to the guild so I have no problem ignoring them or refusing to drag somebody through something, and the first time I get flak for anything I'll just leave. For now, I'm still enjoying mrez and the gathering bonuses.