Remember that the Imperium is insanely heterogeneous.

For example, there are puritan and radical inquisitors. Imagine if these aliens were found were found by a Puritan inquisitor:

- the Emperor is for mankind, not for aliens to worship
- the aliens are probably devious like Eldar and up to some scheme
- the aliens may know about the emperor but their alien minds simply aren't human and we can't let them pervert emperor-worship like this.
- aliens are inherently evil and disgusting, so it doesn't matter what they're doing with the temples, they need to be exterminated.

Then if a Radical Inquisitor found them:

- We can manipulate these aliens into fighting the orks in the same system for us.
- These aliens clearly have no beef with us, let's leave them alone.

The game is set up with this massive setting specifically so that players can tell their own stories using it. Just about the only thing that would seem to be too far out there to me is if the aliens were welcomed into the imperium and treated as well as humans. The Emperor as a god is humanist in the way that Asuryan is Eldarist and Gork (or Mork?) is Orkist - he is there to be the patron and protector of the race.