A high gravity well would dramatically increase the costs and difficulty in bringing in (and taking away) supplies and material. While the natives would have adapted to high gravity, aliens may also find it difficult to even move around effectively. So combine hostile violent natives, high costs of transport, difficultly in exporting anything, including your own wounded, and pacification (aside from just dropping rocks on everything) becomes costly.

Note, even Earth would constitute a high gravity well for Martians. Imagine how much more access to space we would have if Mars was just a smaller Earth with 1/3 the gravity. Getting stuff into LMO would be much cheaper.

Lifted from [Atomic Rockets][1]

> Table 1: DeltaV budget for our Polaris mission.
> 
> Stage******** Delta-v(m/s) 

> Terra liftoff       12,908  
> Hohmann to Mars     5590  
> Mars landing        5030  
> Mars liftoff        5030   
> Hohmann to Terra    5590  
> Terra landing       12,908 
> 
> Total               47,056

As you can see, getting on and off of Earth is extremely costly in rocket fuel, over half the delta V required for a round trip! So if your advanced race must abide by the rocket equation then a high gravity world, even a 1 gee one, may just be too expensive to be worth the fight. Even with a technological advantage, they just can't land enough forces to make a difference. Satellite coverage, small drones, orbital attacks, these things can't pacify like boots on the ground (as the US drone war against several countries clearly demonstrates) unless the goal is extermination of the entire ecology.

  [1]: http://www.projectrho.com/public_html/rocket/mission.php