Again, I'm assuming we both meant "removed" when we said "replaced".

Don't assume. The problem was not that MS provided IE - but that MS used it's monopoly to prevent it's customers from installing a competing product.
(although somehow that pile of crap managed to find its way onto the last three PCs I bought).

Perhaps because IE3, the browser that MS forced on everyone to the exclusion of others, wasn't as good as Navigator - and IE in general is a security risk. The poor quality of MS code apparently made Netscape attractive enough to overcome the artificial barriers to entry that Microsoft created, at least in those cases...
Second, I see absolutely nothing wrong with Microsoft insisting that OEMs not remove IEXPLORE.EXE

Fine. As long as Netscape was an option for OEMs, well and good.

It wasn't an option, though, due to heavy-handed licensing, not any spurious technical reasoning.