Good question.
Since (i believe?) you extract the alkaloiods with non-polar solvents, or atleast mostly non-polar, the alkaloids are in free base.
However, the natural technique for peyote was to boil the cactus for 24 hours or so, thus making the alkaloids migrate to the water - this I believe makes them into the salt form (just from a solution of other plant material as well).
So, it depends on how you plan to take it out...
If you do the modern extraction you will be getting freebase.