Ignoring the synths are people argument, the Institute is pretty "evil." If not evil, unethical.
- Kidnapping and replacing wastelanders.
- Killing wastelanders and replacing them.
- Kidnapping wastelanders to put them in vats of FEV.
- Massacring settlements.
- Disrupting local governments.
- They don't view life above ground as life at all; the Commonwealth is dead, which allows them to use the denizens as guinea pigs.
Perhaps under a more altruistic, or at the very least ethical, leader, maybe the Institute can be a morally good faction. Or at least be a reclusive group of scientists that don't use the people above ground in unethical ways.
Also, I believe you can find the scientist that is intentionally playing God and programming sentience into the synths and stop him. It also seemed implied that it wasn't real sentience, but a mimicry. If [A] happens, feel [B], sort of thing. Then again, are humans any different? Just as synths are bound to their programming, are humans not bound to their genetic programming? Or is personhood granted when one shows that they can move beyond their (genetic) programming?