The actual burner on the Gas Primus Burner is 1.9 inches in diameter, but the under plate is 3.25 inches. The opening on the S-2 is 2.25 inches, so you should be able to fit the burner through, but the plate will stop it from going any further. You would have to rig something up to keep it flush and in place.
The minimum pot diameter for the Clikstand is 4.2 in / 10.6 cm
If you would like to use a smaller pot or cup, please see Clikstands website for suggestions.
http://clikstand.com/i_smallpots.html