Thornton signed a deal with Sunderland in June 2002, a month before his scholarship with Rovers was due to expire.
The move angered Tranmere who lodged a formal complaint to the country's governing body.
The investigation has taken some 18 months to reach a conclusion, with The FA hitting The Black Cats with a £1,500 fine.
The decision to clear Sunderland of two breaches of the rulebook has angered Rovers chief Rogers.
"The time it has taken The FA to reach a decision and the paltry level of the fine show that our regulatory system isn't working," said Rogers. "We have had to wait too long for a decision and this level of penalty obviously won't be a deterrent.
"Small clubs with successful youth development programmes are not being adequately protected - good young players can simply be picked off by bigger clubs and football's governing body will let it happen.
"There should be meaningful guideline penalties in place to stop clubs manipulating the contract system.
"We will be asking The FA and The Football League to give this further consideration."
