Yes, you should be able to do the above. When you guys go to publish your local copies of the team project to your individual AxShare accounts, each project will be automatically generated to a new AxShare ID. This will result in each of your local copies have a different AxShare ID for you to keep separate from the others. Once the ID is created, you can keep generating to that ID without interfering with anybody else's links.
Regarding how to publish with different sitemaps, it sounds like you guys want to be able to only publish certain pages when you're working individually--is that right? Since you're using Axure RP Pro, you have the ability to create additional HTML generators via the "Publish" menu. If each of you creates a separate HTML generator (maybe label them with your names) then you can customize how your sitemap will look when you upload to AxShare and the settings won't affect any of the other generators. Here's a couple of screenshots that should help you set that up:
Once you've created your alternative generators, you should be able to pick which pages will appear in the sitemap and then upload your project to AxShare. You'll just need to remember to select your non-default generator from the configuration drop-down when you upload your project to AxShare.
Hopefully that helps!