Maybe if you have no ships or stations in the system and no army or orbital defense on the planet. But if you reasonably would be able to detect and stop a civilian vessel in your space (in a game with no stealth mechanics) you should have the option to do so.
Two main problems I see with this.
One,
do you have the ability to detect and stop a civilian vessel? The point has been made previously that we have to
infer the presence of a civilian shipping sector due to the fact of normal migration. The refugees could come in via
that, and you literally can't see that in-game.
Now one argument could be that this is gameplay vs. story segregation and you can see it
really, but let me put to you an alternative. Your point seems predicated on the idea that the aliens turn up in one huge Quarian Flotilla like armada which is easy to spot and asplode if you choose. I would suggest that instead, they might turn up in dribs and drabs, as a handfull of shivering passengers at the back of the low-cost transport flights, or even more invisibly as smuggled cargo in the holds of unscrupulous trader ships. This is the model you tend to get IRL, and it genuinely is very difficult to spot. You can't blow up every transport that enters your skies, can you?
And once they land and the pops disperse into the grey economy, all the armies in the world (literally) ain't gonna find 'em.
Two: throwing ships and station strength and military power into the equation makes it a whole lot more complicated. I accept that it's fractionally more realistic, but it seems like a big solution to a small problem.