Hello,
I am sorry I do not see any relation between JoomSEF and the problem you describe.
JoomSEF simply translates some of the Joomla URLs so it should have absolutelly no relation to whether your site will display in some specific browser or not.
More likely, your problem might be in the .js file you mention - maybe it uses some functions / syntax that IE6 does not support. But I would not see a relation to JoomSEF there. Simply try to comment the file out and you will see if the site starts to show up. If so, then you will need to trace the error in the file.