In the film, Dark Alessa tells us that Sharon is "all that's left of (Alessa's) goodness." Simply put, Sharon has no human father. However, many viewers mistakenly leave the film with impression that Colin, the Janitor, is her father because he is implied to have molested Alessa. If this were the case, then it follows that Sharon's birth should follow similarly natural circumstances. As is shown in the film, they do not.
Alessa is assaulted by Colin, the Janitor, in 1974 when she was 9, shortly before her burning, and the concurrent burning of Silent Hill. The events of the film that we see take place in 2004, during which Sharon is also said to be 9 years old. This means she was born in 1995. So for Sharon to be the product of the Janitor's assault on Alessa, it would mean that Alessa was able to conceive at age nine, which is statistically rare, and was somehow able to defy all of human history and remain pregnant for 21 years. Here's why that's obviously not the case:
According to US Department of Health, the average age women begin menstruation is 12, but it is possible anywhere between age 8 and 16*. So for Sharon to have been Alessa and the Janitor's biological daughter, Alessa would have to...
A) Be a statistical anomally in that she's able to conceive at 4 years below the average.
B) Have the incredible ability to maintain that pregnancy despite the physical trauma of receiving 3rd Degree Burns over what looks to be 100% of the her body - a circumstance under which women twice and triple her age would most likely miscarry.
C) Be a biological anomally in the whole Animal Kingdom, in that she gestates for over 21 years before giving birth, surpassing the current record holder, the Spiny Dogfish, who only makes it for 22-24 months.
(Source: http://www.4woman.gov/faq/menstru.htm#6)