Hi Dan,
Hopefully I am understanding you correctly. Right now, you have the token, {{company.Site}}, contain the following URL -
http://www.example.com/?utm_campaign=B2B-Example&utm_medium=Email&utm_source=Marketo-URL-1395
You enter the token in an email, and expect it to add the tracking URL to it, correct? If so, what you need to do is actually break the URL inside the token to two parts. So here is what you will do:
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Change the value of the field company - Site to only have - www.example.com/?utm_campaign=B2B-Example&utm_medium=Email&utm_source=Marketo-URL-1395 (basically remove the http://).
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In your email that you are designing, insert a hyperlink
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The hyperlink that you will put in is: http://{{company.Site}}
Let me know if this is not clear, or if I am misunderstanding what you are looking to do!