I think that would definitely need to be part of the plan. You'd need an escape plan just in case and pray that the alien civilization is not able to catch up with you (which they probably would).

1. Escape plan

2. Bio-war prep. Make it so the planet is uninhabitable unless you are vaxxed against the bio agents.

3. Massive investment in nanotech. You'd want swarm nano-robots, perhaps fitted with micro nuclear warheads lol. I dunno.. just brainstorming.

4. A plan to sabotage the planet so it is totally uninhabitable if all else fails. If we can't live here, nor can they.

Ultimately I think you'd want to use the time to just level up your tech as much as possible so you are not fighting with a pitchfork so to speak.