Well, you do not need to remove it, it is enough to disable com_content in JoomSEF config.
We have installed JoomSEF on several IIS servers with ISAPI_Rewrite (Lite) and it worked fine after some playing with the configs. But mostly it was not as straighforward as with Apache and we needed to adjust the rewrite rules. So I guess the problem is somewhere in the rewrite rules.
Maybe you can write to our paid support to have this done. Also I can put here example of the rules we used on other servers (these were however fot ISAPI_Rewrite 2 series, with v3 it might be easier):
[ISAPI_Rewrite]
RewriteCond Host: (www\.)?yourdomain\.com
RewriteCond URL .*(/|\.htm|\.php|\.html|/[^.?]*)(\?.*)?$
RewriteCond URL .*(?!.png|.gif|.jpg|.css|.js)(\?.*)?$
RewriteCond URL ^/(?!administrator).*
RewriteRule /([^?]*)(\?.*)? /index.php$6 [U,L]