Because your people are dying. You were hired to find a water chip to prevent your people's extinction.
In doing so, you've found a threat of Super Mutants. You're now forced to destroy them to avoid your destruction.
The GECK and the Enclave are the worst things in FO3. The GECK is not really the wonder device it's implied to be. And what would a device that has a bunch of agriculture stuff have to do with a water purifier? Project Purity is unchanged when you deploy the GECK there, and it's never implied anywhere that the GECK purges radiation.
The Enclave were destroyed in the Oil Rig. The remnants in Navarro - wiped out by the NCR. There should be no survivors EXCEPT small groups like the ones in Fallout: NV. Not a huge faction who god knows where they came from. The Enclave in FO3 are encountered in HUGE numbers. I dare to say they are encountered in bigger numbers than FO2 ffs.
Now, about your F1 concerns:
Water thief - Well, nothing really. It's just that there's now enough water for everyone, instead of too few.
About Gizmo, originally this was planned to be a "grey area" in which the evil choice was good, and the good was evil, but this was changed. However the difference is, with Gizmo, it turns out to be a crime sin city like area. While with the Sheriff, it turns out to be nice calm city where people can live.
Nothing happens if you join the BoS. Agree with this one. But going into the Glow does give you nice info imo.
About locations:
Fallout 2 had:
President of the Enclave, who actually was realistic and could be talked to.
GECK.
Vault City.
New Reno.
Sierra Army Depot.
and many more.
Fallout 1 had fewer things.
About being attached? Well, if I am not attached to these people, why should I not nuke them? If they considered you to be one of their own, I can understand. But they don't. You're always a stranger and the people there are weirdos.