I guess the main point against it is the need for secrecy... if an xcom base fired at a UFO, everybody (including the UFO) would immediately know that there's a base right there.
or were you thinking about some kind of automatic interception drone? an interceptor-like defense mechanism that automatically lifts off and engages nearby UFOs (including but not limited to UFOs attacking the base)? that would in itself be interesting, especially when used by the aliens, too... but probably a real pain to code.
I'd like the base defenses to deal meaningful damage instead: the attacking aliens should be wounded and/or killed by base defense hits. so even if your base defenses are too weak to destroy the incoming UFO, they would still decrease the invader's fighting power.