I try not to worry too much about the sugar if it is coming from something like an apple or other piece of whole fruit. I focus more on keep the grams of sugar in prepackaged foods to a minimum.

Concentrate on eliminating ADDED sugar. That is much harder for the body to process.

Two small apples a day should be ok, but don't eat them at the same time (still a lot of sugar at once, regardless of whether it's natural or added) and make sure you always have some protein/fat along with your sugar. I eat a spoonful of peanut butter with an apple. This should help keep your blood sugar more level. Fruit is good for you, but you don't want to eat it on it's own, because that will spike your blood sugar.

MFP unfortunately does not have a way to separate out the sugar from natural sources and the added sugar, so it's something that you have to monitor carefully on your own. I wouldn't worry about the number you're hitting (so long as it's not totally unreasonable) and focus more on the sources of sugar, and how much you're getting at one time/what you're eating it with.

My naturopath did tell me that apples were ok, but not to eat TOO much fruit in a day (like I said, I think that 2 small apples is ok) and not to eat fruits that are high in sugar (bananas, melons, etc... you can find lists of these online).

One thing you could try, if your current diet is not working for you, is to replace one of those apples with a vegetable (I eat one raw orange bell pepper a day - they are a bit sweet like fruit but way lower in sugar) - or a handful of carrots, celery with peanut butter/cheese on it.. something like that. You are still getting your fiber but not overdoing it on the fructose.