The 27-year-old left Villa Park on a season-long loan deal, and the move to the Potters was made permanent in the January transfer window.
However, a clause in his contract prohibits the midfielder from facing his former club tomorrow, and Hughes believes that the stipulation is testament to the Irishman's influence on the field.
He told Sky Sports News: "Aston Villa stipulated that they weren't going to allow the loan deal to be changed unless it was in the contract that Stephen couldn't play against them.
"We had to respect that, or we wouldn't have got the deal done. It is a shame for us because Stephen was excellent last weekend against West Ham.
"But I think it shows Aston Villa understand what a good player we have got. So you can understand it from their point of view - they don't particularly want to help us."
Sunday's clash is expected to kick off at 4pm.