If you need to do an alter table just one time, there is probably no harm in killing it this one time. You should submit the cancel and the alter table on the same line in psql, so that the alter table has a chance to start before another autovacuum kicks off and blocks it again.
There is a small chance that cancelling the autovacuum will cause txid wrap-around and an emergency shutdown of your database which will take a bit of work and downtime to clean up. But if this happens, you were almost certainly in a death-race already anyway.
If you do this often, then you will be storing up massive problems for yourself, including the aforementioned death-race and emergency shutdown.
By the way, your select pg_terminate_backend(16967) should not have a FROM clause on it.