The ps2pdf route implements all interactive PDF features by means of the pdfmark PS operator. An efficient way to remove all interactivity without changing the visual appearance of the text might be neutralizing pdfmark and ?pdfmark:
userdict /?pdfmark systemdict /pop get put
Create a small wrapper mythesisprint.tex and input your pdf with pdfpages:
This will keep the colors but strip the annotations.
It seems that a solution to problem 1 is this one:
For problem 2, apart the solution given by Ulrike Fischer, there is also the option to transform a linked PDF into a PDF/X using Acrobat Professional, as mentioned by MadyYuvi in a comment.
In fact, there is one further ...