You make a really good point, OP.
Leo calling the Nightwatcher out for being a vigilante never made sense to me. Especially because he was off being a vigilante himself as the Ghost of the Jungle.
"... He was doing it in a harmful way, for others and for himself. THAT'S what Leo had issue with... Leo just saw a brute taking his anger and hurt out on others... "
That makes a lot more sense.
"... the way he was dealing with criminals was so aggressive everyone, even the innocent thought he was a threat. Like they didn't see him as stopping criminals, they just saw the violence behind it, leading everyone to believe he himself was a 'bad guy.'... "
I think it's worth noting that, although Leo was also playing vigilante, we never see civilians scared of the Ghost. Only criminals. The villagers almost seem to revere him as their guardian.
Compare that to the chef immediately thinking Nightwatcher was out to rob him, and Raph's line:
"Why does everyone have such a hard time accepting I'm one of the good guys?!" [bold and italics added by me].
This heavily implies that it's not the first negative reaction the Nightwatcher has gotten from civilians he's trying to help.
I would suggest, though, that they're all being selfish to some degree in 07. And I think that's part of the movie's message.
Raph's selfishly choosing to cling onto the glory days instead of helping his family (though he tells himself it's for the good of the city).
Leo's selfishly choosing to hide away in Central America instead of face the music back home (because he believes himself a failure, and then takes that self-anger out on Raph.)
Donnie is selfishly immersing himself in his work instead of being there emotionally for his brothers - clashing with Raph and shooting down Mikey's enthusiasm - (because he's convinced himself that it's what his family 'needs').
Mikey is selfishly ignoring his family's problems and trying to cover everything with humour (instead of being the emotionally mature heart of the family that we know he can be).
And Splinter is selfishly secluding himself from his sons when they need his guidance and intervention the most, and then just selfishly dumps the burden back on Leo when he returns.
I'm not saying they're all the same severity. Just that no one really seems to be trying to fix their family. And they almost lose Leo for good, as a result.
It's only once the family put their selfishness aside that they're able to reunite and beat the big bads.