Is the phrase on the whole used correctly in the following sentence?
The information, on the whole, was inaccurate.
If not, what other ways are there to express it?
This is basically a correct usage: on the whole means generally speaking, all things considered. The one quibble I have is that facts cannot be inaccurate. Facts are, by definition, accurate.
You could say:
For what it is worth, using it parenthetically here is a little clumsy in my view, though certainly not wrong, and certainly understandable. I’d rather you put it at the start: