I might need to increase the maximum number of characters per comment, as the forum I'm putting together is likely to be pretty wordy and I've noticed that the cut-off is slightly on the low side for the sort of discussions I'm expecting.

Is there a fairly straightforward way for me to go into which ever script does that error check (I've glanced around a bit but haven't found it yet) and change the max. length? Are there any negative consequences I should be aware of in doing this?

Vanilla has spam prevention built into the core, so you shouldn't be in too much danger of getting your server overloaded with traffic. The main issue you should be concerned with is that technically the comment field can take as much space as you require - but the more space you allow, the more memory it will take up on your server. As long as you don't allow something ludicrous like 100,000 characters, you should be fine. I'd keep it around 10000 (double the default). But that's just me.