There isn't much long-term evidence on topical 5-FU. It has for many years been a standard therapy for actinic keratoses, which is certainly gets rid of. How well it keeps them away, or whether it actually prevents skin cancer isn't clear. I have never seen any evidence, or suggestion, that it causes cancer either.
I do not believe there is any confirmed trials showing 5-fluorouracil to be carinogenic. By inserting into the DNA in place of uracil, it renders the DNA unusable thus killing the cell. It has not been shown to promote cell growth.
The form of the drug you are using is topical and is thus less likely to travel to distant tissues and cause damage.
If you are concerned about the drug speak with your physician as there are other alternatives for treating AK. One option is cryotherapy if there are only a few lesions. You can also have dermabrasion which is quite effective with only 20% percent having a recurrance after 3 years. There are other creams but the 5-fu preparations seem to be the most effective, resolving the lesion in over 90%.
To answer you quetion, the chances that an AK will turn to cancer within a year is about 1 in 1000. However 60 percent of all squamous CA starts out as AK. By destroying the lesion you can prevent this transformation.
You can also reduce your sun exposure and use sunscreen daily. A trial showed that with application of sunscreen daily your chances of developing AK fall by 51%