[Suicide Junkie]

The allowed projects should definitely depend on the facilities at the spy's current location.

Context-sensitive projects:

A project to temporarily take over a weapon platform for example ... It could fire a volley at random ships in orbit, using whatever weapons the enemy designed into the platform.

If the spies are on a world without organics farms, it should be impossible to sabotage organics production.
Without a spaceyard or resupply depot, it should be similarily impossible to plant bombs on ships.