To quote one of my old Planescape rulebooks:
"Don't. Mess. With. POWERS."
One might do some harm to an avatar or incarnation of a deity. In order to actually do in a deity would be extraordinarally difficult. Remember that (in most settings) divine beings to some degree exist on multiple planes of existence, drawing on the power/faith of worshipers/devotees numbering in the thousands (on the low side). Even mythic PCs don't have that kind of gravitas. They might manage to attain some stature as a "little god" (as per Exalted), but that is still a far cry from Ra or Indra.
Alignment definitions are very problematic and culturally biased, especially when trying to pin down "good" and "evil". IRL, Vikings, Crusaders, or the Conquistadores did HORRIBLE things to their fellow humans. Mind you, from their native cultural perspective, their acts were seen as perfectly justified, normal, or even noble.
So the way I personally approach alignment is on the more objective Law>Neutral>Chaos spectrum/axis rather than the comparatively subjective Good>Evil spectrum (this outlook is heavily influenced by my exposure to the old Planescape setting). A lawful character/race is predictable and set in their ways. A chaotic type is more--well--random. A neutral type can be counted on to behave consistently in either a lawful or chaotic manner in specific circumstances.
Since magic has come up several times...
Going back to the old Planescape system, magic works in subtly different ways on different planes. Even in current Pathfinder rules, there are (rough) game mechanics for high- and low-magic regions that players may have to interact with. In the GM Guide, if I recall, there are rules for setting up nul-magic planes. Planet-hopping adventurers/cultures will want to keep track of what areas are which.
What I'm getting at is that sure, one can have a high level of arcane gadgetry and flash that bend and/or break the laws of physics, but if those same arcana are prone to fizzing out or going haywire just because you've traveled to a different planet, you need to have plenty of mundane gear to fall back on. What was if Han said? "Nothing beats a good blaster at your hip, kid."
Though I don't want to be so overflowing with races that never get any attention. That's part of the problem I have with Golarion. Catfolk, Vanara, Oreads, etc pretty much never get any attention besides the occasional throwaway NPC. Hell, even Dwarves and Gnomes don't get much love.
Re-imagining classic races/monsters is a good way to go. How about this: Dwarves and Gnomes are actually the male and female members of the same species? Or star-faring Beholders, Mind Flayers, and Derro? Hobgoblins would potentially make great analogs for Klingons.
CJ Cherryh's come up with some very solid aliens in her books, both humanoid and non-humanoid. Her Faded Sun trilogy gave us the Mri and Regul (both humanoid), and her Chanur series the Knnn, T'ca and Chi (non-humanoid methane-breathers), Mahendo'sat, Hani, Stsho, and Kif (humanoid). These are the series I'm most familiar with, though she is a prolific writer--lots of material to draw from.