It's about form and content.
As I have opined on another thread, soaps are dramas, and often take a moral stand when working with social issues - wrongdoers rarely escape punishment for instance. In this 'cot death' scenario - I have to admit I don't watch EE so my opinion is based on what I have read - the furore appears to have been caused not by the cot death storyline, but by the ongoing reaction, which some people feel infers that cot death mothers become deranged baby-snatchers - hence the complaints to the BBC.
I do feel that these issues are not comparable simply because they have caused complaints and media attention.
My argument against Frankie Boyle is that he is producing socially unacceptable material using personal attacks on balemess individuals, under the cover of 'edgy comedy', whereas in fact it is neither edgy or comic - simply unacceptable.