For me, I think it would be an issue of how hopeless I think the novel is. Does it need a completely new outline and structure? (Was there an outline in the first place? If not, that might part of the problem.) Do I need to spend more time with my characters? Usually I don't do character sheets, but if I feel like I don't know them well enough to make them real people, then maybe those would be useful.
If I had a novel that seemed like a mess but could still have potential if I re-plotted it completely, then I'd re-plot it before writing anything more of it. Then I'd decide: do I want to keep writing from this point, finish up the new plot, and then go back and fix the rest? If it looks like too huge of a nightmare, I suppose I'd scrap the whole thing and start fresh. This would be painful, with pain directly proportionate to word count. But if I thought it was so far gone, it might feel better and ultimately go faster if I just started from scratch. And the end product might be better.
However, if I thought my basic structure was okay and things just needed some serious smoothing down the road, I'd write the crappy first draft and then do major rewrites.
If you suspect, however, that what's going on is not indeed a true mess but actually your inner evil critic sitting on your shoulder, then flick that critic away. And I know this is going to sound flip, but you just have to let yourself go with what feels natural in the first draft, and then worry about all the fixing in revision. Otherwise you may find yourself completely stalled and frozen by anxiety as you try to appease the inner editor.