So the Unsubscribe HTML from Admin > Email in Marketo looks something like this:
<p><font face="Verdana" size="1">This email was sent to {{lead.Email Address}}. Please do not <a href="%mkt_opt_out_prefix%UnsubscribePage.html?mkt_unsubscribe=1&mkt_tok=##MKT_TOK##">unsubscribe</a>. </font> </p>
So long as unsubscribe footer is placed using the Unsubscribe HTML field in Admin > Email, and it includes the URL parameters mkt_unsubscribe=1 and mkt_tok=##MKT_TOK##, then I *believe* it will exclude those link clicks from reporting, and still create the Unsubscribe From Email activity in the lead's activity log, and add to the unsubscribed column of the Email Performance Report.
Of course, you'll want to test that thoroughly.