Hi Cam,
We have multiple business units sharing the Marketo instance, and 3 of those business units share a website. For the websites that are separate, everything is pretty straightforward and we have no issue.
For the 3 business units that share a website, we have some complications. Here is how we accomplish it.
(a) On general pages, such as the home page or Contact US page, we have a form where a person must select their interest from a drop-down list. Based on what they select, their form gets funneled to the correct business unit's instance
(b) On product specific pages where the page is very clearly dedicated to a particular business unit, our web developer used some java script or code that tells the form which page its on. You could do this using hidden fields in Marketo.
Now, I will say that in regards to the cookies and web activity tracking. Suppose I have a lead 'john@xyz.com' in my database and a co-worker in the other divison also has that lead, we might both see his activity in our Marketo instance. Does that make sense? So for things like lead scoring and lead activity. We don't have activity that is triggered off of website visits, so for us its not a big deal.
If you are using that web activity to trigger any action, such as Visits website 3 or more time > Send an email, you will run the risk that activity on another divisions pages will trigger activity from both your instance and their instance.