This is unfortunately caused by the Require default records function of SiteTree. It may be possible to over-ride this function with a decorator. Or, if you don't mind editing core files, you could just delete it! But that is naughty.
It should only create a Homepage when no page with the URL 'home' is found. As long as you leave the page with the URL 'home' (note the URL is normally rewritten to / anyway) it will be fine. When renaming the page to 'Welcome' just click cancel on the change URL prompt. If you want to change the URL to welcome as well your asking for trouble.
You can add SiteTree::set_create_default_pages(false); into your config.
But if the URLSegment 'home' isn't found in the SiteTree, SS will redirect to the first page e.g. 'welcome'. So it is better to maintain the Welcome Page with the URLSegment 'home'.