If nothing inside the home was altered you should not be getting a smell. Personally I'm confused as to why the repair person would have left the original line there and ran another one through a new hole. I would have pulled the old line up, ran the new line (in PVC) and used the same hole in the septic tank instead of creating a new one. Did he seal up the hole in the tank from the old line?
We called Mr. Rooter because we had a leak from our kitchen sink and they responded quickly to my surprise. Mike Farnsworth shows up and gets right to work and doesn't give us an estimate for the work before he started. He ended up replacing a broken pipe in our basement that took 15 minutes and he plunged our tub and sink as well. He wasn't even here for an hour and he charged us $650 dollars! We refused to pay that much because it wasn't reasonable, so he took us to court and he ended up lying in front of a magistrate claiming he worked for 2 hours and did all these repairs, even though after he had left the sink was still leaking and the drains did not work at all!