Thompson and coach Alex Rae took charge of the Seasiders after Ince served the first of his five-match stadium ban for 'violently shoving' a fourth official against Bournemouth in September.
It was a typically feisty Lancashire derby - settled by Ince's son Tom's first-half penalty - which saw Wigan hit the crossbar twice and Latics winger James McClean sent off after he clashed with home defender Gary Mackenzie in injury time.
"The lads proved their worth and they showed what characters they are," said Thompson.
"We'd done the hard work on Friday - we'd gone through how they play and the video analysis - but it's not ideal when your manager isn't here.
"It was a very good advert for the Championship. It could've gone either way. They hit the woodwork and we could've sealed it late on.
"It was two good teams attacking each other and we rode the storm a bit but we hit them on the break while they were chasing the game.
"We've watched the penalty decision again and the referee has called it right. It was a penalty and it was a good decision.
"The important thing was we stayed tight and compact and we had the front three in Ince, (Stephen) Dobbie and (Ricardo) Fuller who gave us something on a break and they gave us a breather when we had to defend."
It took 24 minutes for the game to spark into life, a lofted pass over the top from Neal Bishop set Dan Gosling free inside the box, with the on-loan midfielder tripped by Scott Carson.
Ince duly stepped up and drilled the ball home, before Wigan hit the woodwork twice - Leon Barnett and Grant Holt both heading against the bar in the second half.
McClean was then shown a straight red card late on despite appearing to be stamped on by Mackenzie, which left Latics boss Owen Coyle furious.
"I'm astounded by the decision to send off James McLean," he said.
"For Gary Mackenzie to stand on James McLean while he's lying on the ground and then for him to get up and not touch him but get James sent off is hard to take.
"We've had it a few times on the road this season when decisions like that have gone against us and we'll definitely be appealing that decision.
"They scored from probably their first opening of the game. I can understand why the referee has given the penalty but there was no real touch on the ball from Gosling.
"The ball has bounced all the way through and he's already off balance and he's just collided with Carson.
"The boy Ince finished the penalty well but we had plenty of time to get back in the game.
"We've hit the bar, post, had one cleared off the line and we committed men forwards."