I really wouldn't be too concerned about the sugar limit, assuming you're being sensible and not eating your entire carb allowance in added sugars. Obviously there's the nutrition side of things, but where kcals are concerned 1g of carbs is ~4kcal regardless of whether it's a sugar or a complex starch. MFP is pretty good, but as has already been said, capping sugar also caps your intake of healthy foods - fruit, dairy, veg, etc.
I'm not sure how they calculate allowances - activity does increase the amounts, but the totals go up for all macronutrients and that doesn't entirely make sense. It's a useful tool though, but that's true for any form of food diary.