Using the content pipeline to dynamically create a spritefont for you at runtime doesn't really feel like it's going to do anything terribly differently than a SpriteFont.FromStream method would do. It's still got to build a texture containing all of the characters you want from the specified font. It's going to store it completely in memory without generating the xnb file, but still given that you can delete that file later, it shouldn't be all that bad. It's a hoop you have to jump through because you have to write this code yourself instead of having it supplied from MonoGame, but I dunno, it doesn't seem that big of a hurdle, especially since it sounds like you've got a mechanism in place for managing assets.
It's not ideal for your case, but the reasons for why MonoGame stuck with the Content Pipeline seemed reasonable. They also provide the tools you need to work around this, if you so desire.
I'm wondering if this might not be the best idea. Assuming for a second that you're not going with a breakpoint approach and instead do pure dynamic loading, this is a lot of fonts to pre-load! I can see your concerns. Out of curiosity, have you done any experimentation with some kind of "just in time" loading? Loading everything at once might add that extra second or two to an initialization, but if it's a few milliseconds inside a single update among many to load just the font you need as you're drawing, would that be so bad?
This is speculation of course, I don't know the answers to these questions. Definitely things that might be worth an experiment or two
I can definitely think of a lot of cases where the font you want isn't known at compile time. I do understand why you want this functionality and I agree that it would be nice, but I also understand that for most games, knowing your font ahead of time is actually pretty reasonable. It's only when you want to create supporting applications/designers for game assets that this becomes a bigger issue.
Most of my other experience is in using stuff like OpenGL (which I don't think has any direct built-in text support), or looking at engines like Unity. For the latter, from what I can see, they're doing all the stuff that you would be building for you... but I don't think Unity and MonoGame are the same kind of thing.