I doubt this was the reason, personally. If it was a glaring, obvious conflict of interest then sure. But this was pretty tangential. Even in his decision to withdraw, the judge says this is a novel legal question in CO. Which means no one has ever raised this type of conflict before, even though I'm sure it has occurred before (judges tend to be friends with lawyers, and witnesses in cases often have their own lawyers).
The judge and the prosecutor were clearly aware of his relationship with McDermott since he disqualified himself from the other case because of it. It didn't occur to either of them that it was a conflict in BM's case, even though the appearance of bias would have been towards the defense.
None of which is to say that BM's lawyers were wrong to raise the issue, just that they could have easily decided not to and no one would have questioned their ethics. And that makes me think that it was a strategic decision. Though I'm a little baffled by the strategic reasons for it. Maybe they have a decent idea who the replacement is likely to be? Or maybe BM was so pissed at not having the charges dismissed that he demanded they find a reason to get a new judge?