It seems Microsoft did funnel money to SCO by first agreeing to pay a $16m licensing fee to SCO for something that they fought against having to pay in the 80s and for which SUN only paid $9m. They also gave $50-60m to an investment firm which intern gave it to SCO.
Beyond financing the fight, there hasn't been any other evidence of their involvement. Anything else is just conspiracy theories.
Microsoft was certainly in full "Linux is a cancer" mode at the time, and even had an executive, Martin Taylor, who was essentially their Linux attack dog. That said, while they were certainly not opposed to what SCO was doing, there's not much evidence that they were the man behind the curtain either.
Beyond financing the fight, there hasn't been any other evidence of their involvement. Anything else is just conspiracy theories.