Shouldn’t be too hard to pull FlightAware data or similar and just not ever shoot within n degrees of aircraft… if it was really much of a concern to start with. Big sky theory.
If it has IR it should also be able to spot aircraft trails but either way if there is any risk of blinding a pilot then they should tread extremely lightly (or non-startup-ish, i.e. obvious potential for "move fast and kill people").
Also, can we get a laser that's collimated badly enough that the beam is ~harmless at distances where an aircraft can be, while still collimated well enough to fry the insect? (In the spirit of "the best radiation shield is r squared".)