It's not Square-Enix's decision to make as to whether it will be a permanent event or not. The collaboration was just that - a collaboration. It could only last for as long as the franchise owner would allow (not sure who owns Garo - TV Tokyo, maybe?).
Capcom was willing to allow the Monster Hunter crossover to be permanent, but it was all laid out in the contract. Since we've been told the Monster Hunter event is permanent, likely nothing short of a lawsuit will allow Capcom to force Squeenix to discontinue the event. I'd say the odds of the Rathalos fight being removed are very slim.
The Garo stuff we were told from the beginning that it was going to be temporary, and were given more than a year's advance notice when the decision was finally made to end it. It's a shame, though, that it wasn't made more clear which lingering items could still be obtained after the event, and how. No one should have to look up two-year-old version updates to learn the specifics of how these items are added to the Calamity Salvager.