The answer is . . . it depends.
If the recipe you are brewing calls for initial bittering and no late boil hops, then yes, you can probably stop it early. The increase in bittering from a 60 minute boil to a 90 minute boil is fairly minimal. The majority of the isomerization for early boil hop additions happens in the first 60 minutes.
If the recipe calls for mid-boil or late boil hop additions, then you are better off keeping to the hopping schedule and topping off water as needed.
Process-wise, this may be an indication that you can reduce your boil off rate and save some energy. Alternatively, you will want to keep track of your boil off loss and update your equipment profile to reflect your boil-off rate so that you won't run into this issue when making future recipes.