the beauty of realID....move a toon or two to the progression guild, and raid other nights with RL friends. Unless you can't raid that many nights a week, in which case you will have to choose. If actual, touchable, meet face to face RL friends, you could have a conversation with them. Wow Raids really not worth losing RL friends over.
Your mother was a hamster, and your father smelled of elderberries.
See if you can have the more progress guild absorb the smaller guild. I have to say that routinely having to pug even 1 person, let alone 3-4 like you are saying, will essentially "kill" any sort of progression. Having to reteach ppl the fights, ect, see if the pug is any good just takes FAR too long for any serious progression to happen.
So rather then an alt group, see if they just won't absorb the smaller guild into it. Players in the progressed group can go in with the second group on alts and stuff- its better to have someone without as much gear, but knowning the fights, then to have someone with gear, but no knowledge of the fights.
"If you look out of the window as a human being, at nature, all of nature is unconditionally and absolutely beautiful wherever it is. Whether it's a jungle. Whether it's a desert. Whether it's the Arctic wastes. Or even your own back garden. The only ugly things you will ever see when you look out of the window are things made by man." - Stephen Fry
The issue is simple:
-try to get your friends to the other guild, have them join it too
or if that's not a possibility
-stick with your friends.
Why? Well think about it, how did you feel when the best dps and the 2 healers left your merry group? Betrayed maybe? And yet, from what you're saying they weren't even friends with you and the rest as much... so how would you feel if one of your friend left your raid group to raid with another guild even if you already had problems?
Not raiding with someone does not mean that you are not their friend.
Just get your friends in the guild, even if they don't start out with a spot. With your backing they will probably get one fairly quickly, assuming of course they are actually skilled. From then it's a simple case of getting back what you put in. When I started with my current guild I was in the alt group with a few friends from our previous guild. However throughout Firelands our guild actually started progressing faster than the so called main group. I'm sure we've all made those types of friends, either in game or out, that we always want to have around, but that takes a willingness from both parties to work for what they want. And if they don't want to come with you, then it doesn't mean you cant still be friends. There is realID, Vent, all sorts of group stuff to do, and of course..../shudder, actual face to face contact.
Science is a way of thinking much more than it is a body of knowledge. - Carl Sagan
False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for every one takes a salutary pleasure in proving their falseness. - Charles Darwin