Actually, it was pretty obvious that although Microsoft Windows was the dominant OS of the time, it would not be in that position forever. You have to plan your software in a way it's easy to port it to whatever you will be running.

You know... There was a time OS/2 was the future.

Also, they could keep their apps modular (unlike what the Visual Studio code generators would give you) so that you could strip the IE-only part when required. Prefering Java over ActiveX and JavaScript over VBScript would also help a lot.