If you have followed the Orsinium main quest to the end:
Spoiler
There is no choice. After the events of the story, Trinimac worship in the public eye has been severely discredited. There is no longer enough wide-spread support for the temple to remain dedicated to Trinimac, and support of Malacath has seen a resurgence.
Gods in the Elder Scrolls are complicated and that legend is just that...a legend.
It's not clear whether or not Malacath is even actually Trinimac or if it's an impostor like Kurog and (Later in Third Era) Gortwog and many others orcs seem to believe.
It's likely that Malacath and Trinimac have always existed and are two sides of the same diety. Wouldn't be surprising, considering there's confirmed dead gods like Lorkhan that have like 5 aspects, with some still being alive and active like Shor in Sovngarde.
If that's the case the struggle between Trinimac and Malacath makes a lot of sense, since both deities represent a lot of Orcish ideology, culture and history.