So I think I have a pretty firm grasp on what H.E.R.O's goals are, but I'm still juggling with what S.I.N is after...I have a few theories:
1. They Really Are Just After Independence
I'd assume this would probably ONLY apply to Ella's children's goal, rather than the higher ups funding the organization. Though obviously WITH strings attached, this would be Zara's marks probably for my next point...
2. Manpower
Ella is on a certain monster side or at least, their goals are aligned; as neither the monsters or her work for each other, it's a (temporary?) partnership. If the marks Zara puts on them truly are to be used as a form of enslavement, it was probably Ella's orders rather than the S.I.N higher ups in order to use the Superhumans as pawns whenever she sees fit.
3. A New H.E.R.O Takeover
This would probably be exclusive to the higher ups at S.I.N, as they have always been a group jealous of Dexter's accomplishments and resources. If they take H.E.R.O down, they are the only group standing to be the new power monopoly of the Superhuman world.
So far we have minimal reasons to distrust S.I.N as it stands. Even Ella wanted no real part of it in the first place but seemed to have Zara interfere a little in how they went about recruit, probably just her own insurance slice. Cole is obviously on board for it PERSONALLY due to beef with H.E.R.O, and Zara I think just views it as fun.
For those wondering what I think H.E.R.O's goal is just in case; I'm like 99% sure they just want to transcend humanity and stop the monsters through research and order. Some have small differences in how to achieve the goal, but overall the end point is still the same. Morally most of the members save for Malik and Clark (and maybe Alexis) actually don't give a fuck about how they go about it. How many lives will be lost, how many test subjects they need, etc. they are NOT a "hero" organization, they're probably more like "Vought" from "The Boys" just with a little less psychotic tendencies for the sake of psychotic tendencies.
Those are just my takes, BOTH are morally bad from the recruitment perspective; S.I.N has those marks that are an obvious insurance, while H.E.R.O will literally torture or even kill you/hunt you down if you don't sign up. Actions wise S.I.N will openly murder, H.E.R.O will discreetly murder. Disagree if you want but I just thought I'd throw them out there and see what you guys think.