Whether McCloughan leaves the 49ers no longer seems to be the issue. By all accounts, change is coming.
Two issues are critical here.
One, it's important to know, at least in general terms, why McCloughan is leaving. There's a big difference between stepping down for personal reasons and losing a power struggle. The latter would suggest front-office dysfunction at the worst time, which would be problematic.
Two, how will the 49ers proceed in the short term and beyond? The draft begins April 22. McCloughan has been a driving force in building the 49ers. Team president Jed York has stressed the importance of having a "pure football man" such as McCloughan running the personnel side. If the 49ers proceed in another direction, York's words should be revisited.