Let's expand your Scenario. I queue as a Healer, I get a group that is on last boss.
We kill the boss.
However, now I still need the first two bosses. So I queue and zone in, guess what? The groups is on last boss, the one I have already killed. So I drop group as soon as I zone in.
Exactly what has this fixed?
Is this a hypothetical situation? If you're solo-queuing you should be getting a fresh instance when queuing again after completing the previous in-progress run. It's not an absolute guarantee, but pretty close to one.
I think the change is absolutely horrible. If I want a fresh instance or just want Garalon, I can queue up and keep doing my dailies/crafting while I wait for the "right" queue to pop.
This new system wastes my valuable play time that I need to get every other (fantastic and enjoyable) thing I want to do in MoP done. Now I have to hope that I am not wasting my time by joining an LFR.
Here are two alternative suggestions:
1) Give people the option to queue for 1/x, 2/x, 3/x or all x/x bosses in an instance. They will be perfectly matched to the instance they want. This might not be feasible given the pool of available players, but still an option
2) Give those who are now "forced" to join an in-progress raid some incentive like you do for tanks and healers in LFD.
Note: the extra valor that you claim is an advantage of losing control of our LFR choices is no great reward. UNLESS of course you raise the weekly valor cap. Why? Because 1 time through LFR and normal/heroics plus dailies is more than enough to valor cap each week.
I lose enough VP to the cap as it is. Where is the VP incentive you were talking about Bash?