My solution to the things not lining up nicely was to give up column alignment completely. In fact, I did that long before I started coding in proportional fonts. I think it was giving up column alignment that opened my eyes to the possibility of using proportional fonts at all. If you don't use column alignment, code looks pretty much the same in a proportional or monospaced font.
BTW my favorite coding font right now is Trebuchet MS on a high-DPI display.
I went through a stint of coding in proportional fonts about 15 years ago. Mostly, I liked it (I used to use Verdana myself, I think?) - you can often get a fair bit more on screen widthwise, which means you can have more files side by side, and the overall appearance is quite pleasing.
Don't recall anything specific that got me to change back, but change back I did in the end. Just a bunch of small things adding up, really, a combination of limitations in commonly available tools, and the repeated need to print nicely-formatted tabular things to the all-pervasive monospaced text console. Swimming against the tide just ended up being more hassle than I felt it was worth.
BTW my favorite coding font right now is Trebuchet MS on a high-DPI display.