There are major downsides to an overpass even if it's replaced with something prettier- stone overpasses are still foreboding and dark underneath. (Though a dramatic arch actually worthy of the Back Bay would be worlds better than what's there now, yes)
But keep in mind there are major downsides to just shifting traffic to the surface roads. Charlesgate E/W would now have very heavy traffic all the time. As someone who passes through the area as a pedestrian daily (and has never used the Bowker overpass itself driving), I'm heavily opposed to removing it. It'd turn what are now fairly easy to walk through and calm intersections most of the time, into a honking overcrowded mess.
And if I were a resident in any of the buildings on/near Charlesgate E/W I'd be heavily opposed as well. Taking all the traffic on the Bowker and shoving it 80ft (W)/250 ft (E) closer to my house, and now making it have to idle, stop, honk, and make additional noise, would not make me happy. Red Sox game days especially will be miserable.
I also don't like mixing drunk college students (Major BU housing + MIT fraternities on Beacon St) with heavy traffic.
The Overpass is certainly ugly, but I think removing it is far worse for pedestrians, residents, and drivers alike.
I'd like to see a replacement. I'd just like them to find some way to avoid having the large stone wall + giant concrete supports that ruin any sense of "park" @ Beacon St currently, and in general do some landscaping of the area. Poorly maintained grass and gravel doesn't help the looks.
I also do think it'd have a massive impact on traffic in the area in general, probably backing up onto Storrow + Boylston constantly.
I would call it highway-era thinking because it appears the decision was made solely by traffic volumes- without the consideration of the continuing blight these monstrosities provide. (Extremist pro-auto thinking demands extremist anti-auto in response)
I don't disagree that it is ugly. On the other hand, "blight" is a term which generally implies to me that it's having negative impacts on the surrounding area....and looking at anything nearby there, you're going to have a pretty difficult time finding much evidence for that.