So these Pandra guys are only bad in name when actually they have a good heart. Too cheesy for me. What's next, Andy would join them for real. I hope the anime doesn't follow this path.

PANDRA exists for the sake of Espers, and a lot of the nature of the organization stems from Hyobu's own background and personality. As a former Child Soldier Hyobu has a very soft heart when it comes to Esper children. He under no circumstances wants them to experience a life like he had and he has gone out of his way to save them. Magi, Momiji and Yoh for example are all war orphans that Hyobu raised himself. After the death of their parents Hyobu is the closest thing they have to a father.

while the nature of the organization is friendly almost family like atmosphere that too is a product of the Major's background. The unit he was a part of in ww2 had a very similar sense of comradery, particularly between Hyobu and Fujiko.

So yes in the eyes of Espers, particularly those who have faced oppression and hardship at the hands of Normals, they are going to seem like good guys.

but Hyobu has very little empathy for normals. As seen in the first two episodes he will not hesitate to kill Normals for his goals. Episode 2 in particular I think shows that as he leveled a large chunk of the city to kill his enemy. Lets face it it is unlikely all those houses were uninhabited. Even in Episode 3 the look on his face when Princess Sophie is talking about her dream of a world for Espers and normals living together shows you what he thinks of that idea.

Hyobu has heard those kind of words before and the very same person who said them to him is the one who ultimately put a bullet in his head.

Hyobu will always give into the requests of a child Esper. It's his nature, he doesn't want any child to suffer like he did. He can be a very friendly and kind person towards other espers. But he is also someone who sees normal humans as a threat to his people. He knows a war between Espers and Normals is coming and he intends to win.

When it comes down to it Hyobu will slaughter a hundred normals to save the life of 1 Esper.

deciding one of your race is worth 100 (really more in his case) of another. Lots of examples I could use (trying not to go Godwin, but its there) would seem ok if not downright friendly to their 'own people'

In Hyobu's case he also has the added motivation of a powerful precog who has predicted the outcome of that very war, an outcome he is rather desperate to prevent