That's easy to say in hindsight, but coming up to the decision, I'd take the chance. It's only a few thousand people and one destroyer.
Perhaps, although I still think they had all the information the needed to know how that was going to go down. The rules of the universe are that capital ships don't need to slow down or stop in order to fire their beam cannons. Putting a second Colossus in front of the node wouldn't have delayed the Sathanas.
And, while I understand the vast differences in what's at stake between that situation and what I'm about to mention, "only a few thousand people and one destroyer" is on the surface a pretty hilarious line coming from one of the designers of a campaign in which a war has gone on for a year and a half without a single destroyer loss, because both sides are so careful.

To respond to your edit in which you restate a point you made earlier:
You keep invoking these radiation/explodiness problems, but there are far more parsimonious explanations I've already presented right here - "The Mjolnir as we saw it had one purpose: to sit outside a node and fire its beams frantically in a very narrow engagement window, probably blowing all its reaction mass, wasting its own power systems, and irradiating itself in the process. That's just not a formula for success on a warship. (Warships also need subspace drives - forgot about that.)"
Sitting outside a node: Given that a node is much larger than a corvette or cruiser, the mjolnir still relies on the mission designer to put any hostile ships short of destroyers exactly where it can hit them. Sans helpful fredding, the non-homing mjolnir sucks at its intended role.
Very narrow engagement window: The mjolnir's linear fire axis is less of a limitation, not more of one, if it's mounted on something with engines.
Blowing all its reaction mass: Not sure what you mean here. Are you using reaction mass to mean fuel/power supply? Or are you saying beams in BP-canon have appreciable recoil that some sort of reaction mass would be needed to counter-balance?
Wasting its own power systems: I put this under stability concerns.
Irradiating itself in the process: Sounds like radiation to me!
