You're basically replacing one problem with one bigger problem.
Surgery is a complex thing, but it's a 400-year-old proven technique that has been extremely enhanced by the available technology.
Such technology allows the Federation's medics (and those of other spacefaring cultures) to isolate a problem and perform precision surgery on just that particular part. The risks of killing the person because of something unrelated are extremely low (i.e. the risks of damaging a lung or the brain while doing heart surgery are very low).
Compare that with the risks of loading a pattern and messing with it. The complexity of such a thing is several orders of magnitude higher and has a lot more risk. An inappropriate manipulation risks a myriad of unpredictable complications, from brain damage, a guy without legs, or with a shattered central system.
Generally speaking, what you want in medicine is to reduce risk and to make sure you only solve and cure disease trying to avoid, whenever possible to mess with non affected areas.
The difference between using the transporter for surgery and for pathogen removal is that the latter is just simple filtering of cells or organisms within the pattern (taking them out) and doesn't work if you can't clearly isolate it from the rest, while surgery is different every time, you need to analyze the problem and then decide how to fix it....
In summary, I wouldn't want them to use the transporter to mess with my pattern if there was standard surgery available.
Edit Regarding Canon:
This is just logical deduction, as the matter stream is a "stream of sub-atomic particles" according to Memory Alpha, which makes total sense. As far as canon references, there is mention of the confinement beam allowing the transporter to isolate patterns, but there is no reference to any clear structure for EACH such pattern. Given that there's no canon reference (that I can find) indicating the contrary, the logical assumption is that the "stream of sub atomic particles" is just that, a simple stream.