I know tomatoes are fruit and thus vegan, but as pointed out in the book they are nightshades which aren't good to consume regularly because of the potential rheumatory damage. My problem is that I love tomato sauce and many dishes which use it. I can't just remove the sauce from all of the dishes because that would render them quite flavorless. Is there a less damaging alternative?

I personally think tomatoes are fine in moderation, and even when I'm really trying to eat "Superhero", I don't avoid them altogether. There's a recipe in Crescent Dragonwagon's Passionate Vegetarian (one of my all time favorite cookbooks!) called "Macro-Red Sauce":

About 3 c. mild vegetable stock

2 lbs (1 medium) butternut squash - seeded, peeled and cut into large chunks

2 small beets, scrubbed and halved or quartered

1 tsp to 3 Tbl olive oil

cooking spray

1 lg onion, chopped

4 cloves garlic, pressed

1 1/2 tsp honey or to taste (of course you could sub agave or brown rice syrup)

2 Tbl red wine vinegar

1 bay leaf

1-2 tsp dried basil

1-2 tsp dried oregano

1/4 tsp dried rosemary

1/4 tsp dried thyme

salt and pepper to taste

Place 2 c. broth in bottom of a large Dutch oven, place vegetable steamer insert into it and add squash and beets. Cover tightly and steam until veggies tender (25-30 min), adding more stock as needed. Let cool slightly, peel the beets. Puree, adding stock as needed until the consistacy of tomato puree. Suate onion in olive oil until translucent. Add garlic and saute for 1 min. more. Add beet/squash puree, honey and vinegar. Reduce heat to low simmer. Add herbs and lots of freshly ground pepper, let simmer until it has consistency of a sauce. Taste for salt, additional herbs, acidity. Add more vinegar, salt, herbs accordingly. If possible let the sauce "age", refridgerated, for 6-8 hrs before serving. Remove bay leaf before serving.

I haven't tried this yet, but there's a product called Nomato that might be perfect for you:

http://www.nomato.com/products.htm