Firstly, although Charrington seems to be more senior than the Thought Police thugs that are beating Winston, it's not clear what rank he holds in relation to the overall organisation structure. He may simply be one step up from them.
His shop is, as you've indicated, a honey-trap designed to entice party members who're swaying toward subversion. Note that we see illegal items openly displayed:
He could guess, however, that the book was much older than that. He
had seen it lying in the window of a frowsy little junk-shop in a
slummy quarter of the town (just what quarter he did not now remember)
and had been stricken immediately by an overwhelming desire to possess
it. Party members were supposed not to go into ordinary shops
('dealing on the free market', it was called), but the rule was not
Later, Charrington attempts to subvert Winston further by offering him additional forbidden items and (horror of horrors) a private room with no viewscreen. Had Winston not returned, it's likely that his other indiscretion, purchasing the blank book, would have simply been overlooked.
As to why a member of the Thought Police would spend their time running a shop, the answer is that it's probably part of normal Thought Police procedure for members to take turns undercover running different establishments, each with the aim of identifying party members who've gone off the straight and narrow path. How better to find out about subversives than to be among them?