You're not alone, I partially sympathize with Team Plasma as well (I'm concerned with animal welfare in real life). I initially had a hard time understanding Team Plasma, as their situation would seem to create cognitive dissonance in the grunts using Pokemon to free Pokemon. And then I realized they seem to be modeled after extremist animal welfare groups in real life. The way those groups see it, the only way to prevent future abuse is to get rid of situations that could potentially create them; all of the negative man/creature relationships outweigh any positive ones.
Now back to Team Plasma specifically, for those that actually believed in Pokemon liberation, if the only way to free Pokemon from abusive masters was to use their own Pokemon, then that was the way it had to be. It was a temporary servitude that was furthering the betterment of the world. Plasma Pokemon were being forced to serve for the greater good, and once they had helped create their ideal world, then their Pokemon could also be set free.
Or at least that's how I see it.
This mindset only applies to those grunts that actually believe in Pokemon Liberation, not whatever world domination plans Ghetsis was actually trying to achieve.
