The former Baroka FC forward was on the bench against Cape Town City on Saturday, having barely featured in the second half of 2016/17 after clashing with club management.
Mncwango was suspended by chairman Johnny Mogaladi after bemoaning his treatment to the media amid interest in his services. He was then barred from training, which annoyed Molekwa's unsettled colleague and head coach Luc Eymael.
Mncwango, who scored three goals in 14 appearances this campaign, last played for the side against Maritzburg United on February 8.
However, he still has a future at the Limpopo-based outfit, according to Molekwa.
"Thobani is very much of the team, he's a good player, good mentality. If you can check the way he has been performing at training it is just he was unlucky sometimes," said Molekwa, who steered the club to a best-ever sixth-place finish after Eymael resigned in March. The Belgian has since returned to City on the orders of the PSL's Dispute Resolution Chamber.
"The way he's been working, he's a player that is very much important and he's a player that you'll like to have in your squad. Obviously, we haven't discussed everything but we'll do that this week and also give all the players the official closure. We are also going to tell them when are we coming back but it is something that we are going to discuss."
The 29-year-old was the second top scorer in the Absa Premiership last term with 13 goals in 29 outings, just one goal behind Golden Boot winner Collins Mbesuma.