Maybe you should read the book again. Tensions were high in the tower after Anders' terrorism and the attempt on the Divine's life. Rhys had already been summoned by the Lord Seeker and found suspicious due to his connection to the Libertarians. (as it turned out, he was right because Rhys ponders at the end of the book that Cole was, most likely, using him to commit the murders.)
Then he leaves the rooms at night, deliberately distracts a Templars which implies he didn't want them to see what he was doing, releases destructive spells in the basements of the tower and refuses to answer the Knight Captain's questions when confronted.
The only reasonable thing to do was to confine him.
That is not a reason to put the guy in prison.
MisterJb wrote: He was breaking curfew and throwing destructive spells around after a member of his political group attempted to assassinate the Divine.
Anyone in Thedas would have locked him up.
Answer not true. That is not what he was charged with. He was charged with being a murder suspect and they had no proof. You wrote generalizations but did not write the actual charge. You can’t put someone in jail because tensions are high. They didn’t care about the people murdered. They wanted names of blood mages. They had nothing on him. They were going to let him die of dehydration and they didn’t have the evidence for murders. Remember all the murders already happen. All were stabbed with daggers. The Lord Seeker wanted names to tie more blood mages with the attempted assassination of the Divine.
Misterjb wrote: This being the same book where, after the mages made some noise, Lord Seeker Lambert released a suspect in an ongoing investigation?
No again. Wynne force him to release her son with an order by the Divine.
If you didn’t catch this Lord Seeker was the villain.