You know what grinds my gears? Trial judges taking their sweet ass time making a straight-forward ruling like this one should be.
Did you mean to ask how it would disadvantage his defense? If so, that's impossible to answer, because it obviously didn't/doesn't at all. The theory is that the relationship was a/the motivation for pursuing the case and/or creates an improper incentive to try the case no matter what. At least that's the idea behind the disqualification statute - prosecutors are supposed to only care about obtaining justice.
It's dumb as fuck for multiple reasons. First, a grand jury indicted defendants. Second, this case was always certain to go to trial. Third, everyone knows Trump is guilty. Fourth, Wade was already making good money from his practice; it's not as though she gave her unemployed bf a job. Fifth, they're no longer seeing each other.
The judge seems most concerned about the "appearance of impropriety" tainting the public's perception of the case. Couple of problems with that. First, the applicable law seems to require an actual conflict, not just the appearance of one. Second, everyone who might question the legitimacy of the case based on these facts has believed it was a sham from the getgo. This whole issue's been a big, pointless waste of time.