Go for it. Stainless steel is quite stick-friendly already, and the added unevenness from the microtool won't really make a difference. Also, this is a soup pot, and the side instead of the bottom, so you wouldn't really expect sticking.
I'd suggest that you try to make a wide marking, not just a groove, for sanitary reasons. You want water to easily come in and wash out everything, so a width of at least one milimeter would be good, two milimeters better. You can just align the bottom of the mark with the needed position, so you don't have to eyeball the middle of a wide mark.
This will be a bit difficult to do if the pot diameter is small, because your router-stick-on-thingy* is supposed to go onto a plane surface. But maybe you'll find a way to do it. In any case, really use a router bit with some width, not the side of a small cutting wheel. Ideally, the resulting mark will have an oblong cross-section, with a flat bottom, vertical sides, and a rounded connection between bottom and sides. If you don't have such a bit, make it vertical with a 90 degree angle at the bottom. The worst option would be a v-shaped groove, that would gunk up quickly, like a condo for bacteria.
And if you find it not so practical, either because of the "catches dirt" possibility or because you can't find a way to hold the bit vertically to the surface one centimeter above the pot bottom, consider acid etching instead. Chloric acid at home-improvement-store concentrations should work on domestic grade stainless steel.
* sorry, that was my best try translating Oberfräsenaufsatz into English. If you have the microtool, you know what I mean.