It was seemingly pointless to destroy Morrowind as well, given that its not really changed anything in-game yet. However, Bethesda is known to always have the rough plots of the next 2-3 games planned out, they do things with a purpose. If they do make Ronto being destroyed canon, its likely for some reason in the long run.
I don't deny its a guess.
Well given that
A. Its mentioned on a terminal in The Citadel that the government tried to recover a UFO in Maryland.
B. The leader of the Outcasts accepts alien tech as part of his quest.
C. The Enclave are found investigating alien power cells near Fort Bannister
D. The Enclave are known to have alien power cells, and an alien blaster, in their base at Adam's Airforce Base.
E. Alien power cells can be found in Olney Power Works, with a cut note explicitly stating they were studying how they worked.
F. There is an entire DLC about them.
G. The Fallout 3 game guide suggests the Enclave may have gotten a lot of their advanced tech from aliens, something supported by their study of alien tech in points C and D
Aliens seem to be canon.