What I'm hearing is people saying they want to be able to stay in their group finder queue while they're playing a warzone and that it no longer possible. I'm assuming here, but the accepted practice seems to be that you will enter your flashpoint when the queue pops whether you're in the warzone or not, or you will enter your flashpoint after you've completed your warzone. Is that right? Because if that's right, that's the most asinine thing I've ever heard of. You want the ability to leave the warzone you're in, in effect hurting 7 other people who are sharing that time with you, (clearly their time isn't as important as yours) so you can do the flashpoint you want to do. OR, your plan is to make 3 other people wait for you, (clearly their time isn't as important as yours either) to begin their flashpoint while you finish your warzone? Man you're just the most important person in this game and everyone should schedule their play time around your schedule and be honored that you've chosen to play with us eh?
The loss to a warzone team is minimal when warzones backfill instantly or near instantly.
If you're a DPS, it can easily take anywhere from 1-3 hours for a HM FP queue to pop (especially if you're trying for a specific FP like lost island).
Seriously sit for a second and think about the alternatives. You can now choose between sitting at your screen and doing ostensibly nothing with other people (you can't group or PVP at all) while you wait for group finder to cycle through all the DPS who queued before you. It makes a lot less people want to queue for one or the other, which increases queue times even further.