I always thought Trinimac was removed from the Altmeri pantheon, because they viewed him as being tainted by Dunmeri influence. Plus, his failure to stop the Velothi exodus marked the begining of the splitting of the Aldmer.
According to Varieties of Faith, he's still part of it. It includes this:
"He [Trinimac] vanishes from the mythic stage after this [corruption by Boethiah], to return as the dread Malacath (Altmeri propaganda portrays this as the dangers of Dunmeri influence)."
He seems to be a part of their pantheon, but probably in the Mythic sense rather than the "currently receives worship" sense.
"We get serious about fictional girl underpants, and kid around when it comes to topics like world hunger." ~Teepo on CAGN