Doesn't matter, humans first. They were just using Shepard and the Lazarus Team. Read the reports after a mission and you'll see that they were getting data that they (cerberus) wouldn't normally get by normal means.

Thanks. I think. I will do so, as I'm curious now that you explain it

Jack Harper AKA The Ilusive man confirms that Shepard and the entire lazarus cell was just a means to an end. By ME3 there actions were no longer there own and can’t be Held accounted for seeing as they have become indoctrinated. Gavin Archer is the worst person ever and they were fine it tells you all need to about them.

What you say seems rational, but even before 3 everything seems a bit suspect. Such as what they did to biotic children, for example

Cerberus isn't really shown in a good light still. Throughout ME2 literally everyone shows concern over Shepard working for them or them even joining up to begin with. Not to mention the multiple instances like in Jack's loyalty mission and the Overlord DLC.

To put simply they're an organization that believes the ends justify the means even when it comes to their own human experiments. It's also an organization that believes in Human supremacy, despite their best efforts to say they only believe in the advancement of humanity.

In ME2 they just so happen to be fighting for the right cause.