It seems Bolsonaro was lying. Moro's resignation did not come out of a vacuum, there was talk about it for a while and when Bolsonaro sacked Valeixo he knew a resignation could come. Likewise there was talk about political pressure on Valeixo for a long time so it can't be a personal desire to leave. Moro leaked Whatsapp correspondence with the President to the media. On them Bolsonaro links to a piece of news about the Federal Police weighing down on 10-12 of his deputies, and says "one more reason for a replacement". Moro pointed out that this was by the Supreme Court's orders.
The investigation itself is part of the Supreme Court's fake news enquiry, which is controversial and part of their tendency to overreach, on the same line as their gag orders on a news site last year.
Moro might be lying about not trading Valeixo's stay for a Supreme Court naming but there isn't more information on that.