Let me just say first of all, Brandon (not his real name), that I don't believe guild splits are necessarily a bad thing.
As a case in point, my own guild underwent a small split at one time. It was a matter of certain players in the guild who just never got along with a few of my officers. A couple of my officers are no-nonsense types. They don't coddle people, and they don't deal with emo very well. The players who had a tendency toward emo were sort of a subculture within my guild. They were all very close, and whenever one of them felt they were being treated unfairly, they all got involved. So any small bit of drama quickly became a Big Deal. We had acquired most of these players through guild mergers (something I'll never do again), so we had no idea about the problems they were going to bring us. They had a lot of enthusiasm for the game and many of them were very nice people, but most of them weren't particularly effective players. So when they came to raids there were sometimes clashes between them and some of my officers, who expected a better performance.
The bitterness between the two sides grew, and it seemed like no amount of diplomacy on my part could bridge the gap. Finally, one of them decided she had had enough and quit the guild. Later that day, she asked me to let her back in, but I had had enough too. So she decided to start her own guild and took with her just about all the people who had been causing trouble. My guild has been virtually drama-free since, so the split wound up being a very good thing for us in this case.
Admittedly, sometimes these splits can get ugly. Unfortunate words are exchanged. Items are stolen. And basically the whole thing crumbles apart and the officers are left to fight each other for the scraps of what remains like the squabbling heirs of a deceased emperor.
But it sounds like Brandon's split was more on the amicable side, so count your blessings! If there is fundamental disagreement among the leadership, and you have tried and failed to reconcile your philosophical differences, going your separate ways can be the only real solution. Most people are going to fall into one camp or the other, but Brandon is one of the unlucky few stuck in the middle.
But because he is close to both guilds, and has had some authority as an officer, he is in a unique position to be an effective liaison. Even largely self-sufficient guilds still face times when they need just one more person to fill in for a raid, or have someone who can do one rare high-level enchant but not another. The person who can reach out to find one more DPS class or broker trading a Mongoose enchant for a Soulfrost can be quite valuable.
But he still has to make a choice. It seems to me that in this case, the decision Brandon makes is almost irrelevant, provided the guild you don't choose to join can forgive you for it. If you stay in your friends' guild, the other guild may still ask you to help them out in raids. If you join the raiding guild, your friends will still be there for you when you want to party up and goof around with them. So "having your cake and eating it too" is largely a matter of how reasonable everyone else is willing to be.
If you have alts, you can make a compromise. One way to handle this could be to have your main raiding character in one guild, and all your other characters in your friends' guild. If you go this route, never ever switch your main raiding character -- your friends aren't there solely to help you gear up your alts so you can then move those characters over to the raiding guild too. That's a surefire way to make them resent you. Also, I don't recommend being an officer in either guild if you have characters in both. Your divided loyalty will make you suspect when it comes time to make difficult decisions.
Of course, you could always try sticking it out with your friends, recruiting a few more like-minded people, and giving some "casual raiding" a go with them. Since 2.1, Karazhan has gotten a lot easier. Ten players with endgame 5-man rares and a voice chat server can do virtually any fight in that instance, and it keeps getting easier as you gear up in purples.
In the end, if you have no other choice but to decide once and for all between the guilds, I always recommend standing by your friends. After all, WoW won't last forever, but friends are for life!
Send Scott your guild-related questions, conundrums, ideas, and suggestions at firstname.lastname@example.org. You may find your question the subject of next week's Officers' Quarters!