I agree that having line numbers be less prominent is generally a good thing. In the case of the editors/IDEs that I use regularly (including SciTE), I can easily change the font of the line numbers separately.
In the case of Geany, I think that those who either can't or don't want to recompile their editor (for example with Colomban's patch), the simplest and best solution is to just learn to deal with it. I mean, even though I like less prominent line numbers, the existing ones are not *that* bad, and you can get used to it. And you can try little things to make them less prominent, like adjusting all the text to have greater spacing between lines. (I don't remember if you can set the line spacing separately or if you have to pick a font with more built-in space.) Yes, the trade-off is you can fit fewer lines of code in the same screen space.
If it's an easy change to make in the official Geany distribution, I think it would be nice to be able to adjust the line numbers separately. Geany already has an enormous number of settings; one more won't hurt, in my opinion. ;) But if it's too much of a bother, or if it's going to be the setting that breaks the camel's back, then I would say leave it alone.
If we're voting (using Python-dev convention, which I'm sure is borrowed from somewhere else), I'm +0 on adding this setting to Geany.
John