Thompson has had an operation on a knee cartilage problem which he underwent while serving a two-match ban.
Rovers boss Graeme Souness told the Lancashire Evening Telegraph: "If things go to plan and we pick up some more points in the next few weeks then, ideally, I'd like to rest him.
"We could rush him back but I'm being told that that could take months and maybe years off his career and I wouldn't want to do that to anyone."