You're signing into a battle.net account. Battle.net checks your account for a license or active sub (depending on the game) and allows/denies access for that specific game. Each game is separate from the rest.
In other words, cancel away. Wow sub has no affect on any other game on your account.
If you need confirmation of this, then I have that too. I got D3 from the WoW annual pass. I let my sub lapse after the AP ran out and I can still play D3.
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