The Pippen sign-and-trade benefited Pippen and the Bulls. That's not a favor. Reinsdorf didn't renegotiate contracts out of principle, but because he didn't want to pay players more money. Same reason they decided not to bring back the whole old squad in 1998.
Jordan also made close to 10x his basketball salary per year from endorsements by 1990 when he was still grossly underpaid. Pippen's marketing star was far, far dimmer, and he hadn't secured his long-term fortune off the court.
It definitely was a favor to Pippen that his own agents requested. If a straight trade to Houston had occurred, the max that he could have been paid was a four year, $45 million dollar deal (11.25 million a year). The sign and trade enabled Pippen to sign a five year, $65 million dollar deal (13 million a year).
I agree that they didn't want to pay the squad in '98 but it absolutely was Reinsdorf's personal policy not to renegotiate contracts. He used that excuse on Jordan as well. And honestly, while it certainly would be nice to pay the people who are making you all that money, no one has any obligation to renegotiate a contract once it's been signed.
Your last statement is true as well but has no bearing on the fact that Pippen acted like a spoiled brat in delaying his surgery that summer. His teammates all said they understood but they also all felt it was a bad decision.
Lastly, fun fact, Jordan was so underpaid that when it was all said and done, Pippen ended up making more money in his NBA career by almost $20 million! Only counting basketball salary of course.