Originally, it was spelled practicioner. OED provides examples of this spelling as recently as 1735. This was probably the original spelling based on its etymons: practician n.; French practicien
1735 In Physick there are, and have been many happy and lucky Practicioners who knew not so much as the Christ-cross Row.
- South-Carolina Gazette · 1732–1775.
The change to -tion was likely part of a switch to the Latin suffix which uses a t, and which became a standard spelling for such words that had obsolete forms spelled -cion. OED's entry on coercion offers a foot-note clue.
The current spelling [coercion] is deceptive, suggesting formation < coerce + -ion. This no doubt led to the retention of the c when all other words with the mediaeval spelling -cion, were altered to the Latin type in -tion.
Wiktionary confirms this explanation with added detail:
The Middle English -cioun became -tion in Modern English under the influence of the Middle French -tion and original Latin spellings.
The two remaining exceptions are "suspicion" and, as discussed, "coercion."