This example contains a comma splice (two sentences joined by a comma).
You’ve got two options here: you can replace the comma with a period and begin a new sentence (don’t forget to capitalize It as the first word of the second sentence!), or you can replace the comma with a semicolon, because in this example, the two sentences are closely related.
The use of a semicolon versus the use of a period does have some effect on the flow of the sentence/sentences. Two shorter sentences will have a more choppy/abrupt feel than one sentence with a semicolon in the middle. Which you choose depends on the result you want.
Every morning she woke in agony; it had been this way for as long as she could remember.