Is this going to muddle the hero's journey and conflict in the story?
Quite the opposite - at least if he has a reason to do this
Your character shouldn't join the antagonist group out of a whim. This should be treated as a major event. A turning point where you need to show the conflict of your hero in joining the people they despise.
Is there a common evil that the hero can only hope to compete against if he joins forces with his antagonists? The enemy of my enemy is my friend.
You might also want to make sure that the reader is clear about how long the protagonist is planning to join the group. Does he have a specific goal he wants to accomplish with their help? A hero probably wouldn't join the bad guys who hurt him before forever. Maybe he is waiting for a chance to destroy from their innermost centre by learning how they operate?
This could be used to show more conflict in your story. Maybe the bad guys are not all that bad. Or at least not every single one of them is bad. Maybe your hero finds valuable friends on which he can rely behind enemy frontlines.
My protagonist will likely reform the group that he joins
As before, ask yourself: Why would he do that?
What is his reasoning? And is it easy for him?
This is a good setup - if you think long and hard about the reasons and show your reader the inner conflict of your hero in doing this. Emphasize that this decision is not easy and try to repeat this throughout the arc, in ever changing ways.
Maybe at first he has thoughts about destroying them. Then he wants to help them. Then he wants to start another group to show them how to do it. And in the end he arrives at the decision that reforming them is the best way to go about this.
The details and depend on your story and the way you want to narrate it, but the setup is promising and leaves room for lots of opportunities - if you are narrating the resulting conflict as clearly as you can.