Ha - I'm going through the same thing. I want to write a HIDDEN feild only when certain other checkbox fields are marked as TRUE, so I need the new Forms 2.0 JS API, which means I need to offer that form through a <script> tag. But then, no more prefill, which also defeats the purpose. I tried embedding it in a Marketo page, no dice. Tried embedding it directly in the HTML of a marketo template, but still no.
I can probably figure this out using Smart Campaigns, but sometimes the quick JS is just way easier and more elegant (firing a smart campaign on "fills out form" still feels like it might "miss" (I'm sure that's just me).
Currently wondering if there's a way to combine the Munchkin API "Associate Lead" function to grab data from MKTO cookie and then populate the form. But that solution (if it's possible) looks a little too much like something held together with duct tape :S