The team's deputy principal Bob Fernley made this clear when drivers Esteban Ocon and Perez qualified 18th and 19th for Sunday's Hungarian Grand Prix.
"There can't be any animosity," Fernley told www.autosport.com.
"Whatever happens, like everybody else, 'Checo' (Perez) is entitled to be paid.
"Unfortunately we were not in a position to be able to pay him, and patience runs out for everybody. So, that's a process.
"I don't think we in any way look negatively at him. The responsibility for payment is on the team, not on Checo.
"He's been put in a difficult position. I think we have to respect his position, and not criticise it."
Perez's Mexican sponsorship has been a mainstay of the team's operations since he joined in 2014 and helps to ensure he is paid his salary.
However, delays in payments led him, through his management company, to take part in the winding-up order that was heard in London's High Court on Friday.