Harper’s Ferry is in Virginia.
The arsenal was federal property and Virginia had no legal rights to it. Sending troops to seize it was an act of aggression on the part of the commonwealth. The first act by either side, so I don't see why you complain about federal troops in Alexandria. Virginia had been actively participating in the rebellion for more than a month prior.
And while the referendum may have been on May 23rd, the Confederate Congress admitted Virginia as a state on May 7th. I guess that referendum really didn't mean anything at all, did it?