When you employ micro-identity iconography, you tell the user that they're in a new, self-contained area. Users will not expect the 'home' icon in this space to take them to a different area of the site, even if it is one they visited earlier. And they will certainly not expect a link to suggest one location and provide another.
The microsite doesn't have it's own URL (it's www.mainurl/microsite)
Don't worry about this. Few users look at URLs much. Even fewer care about them. If it really bothers you, give the microsite its own subdomain (this is what they were originally for, after all).
The microsite has the same logo and header style (so you almost can't tell you've left the main site)
You may want to better differentiating the microsite identity, else you risk leaving users unsure 'where' they are in your content. Common practice is to maintain the shape and forms of iconography, but swap out the colours. This will do a better job of communicating that the user has moved to a different space, and, as a bonus, it mitigates your fear that the microsite logo might get confused for the main site logo.