Yes, removing inactive bases from systems that are overly populated harms nobody and is always done by interacting with folks around. Matter of fact, as you well know already from another Discord, the Falcon dec will be removed soon as the base does actually help some folks around, which is completely fair and fine. The reactors and GMC, on the other hand, have been decaying for the better part of this month, with no traffic to them.
I will let history be the judge of whether or not removing a few inactive bases is good or bad for the game long term, considering how easy they are to construct and how prevalent they are anyways.