Personally, I don't see the problem if Walsh believes Sky to be clean. If he genuinely believes Sky to be clean and has put pen to paper (or committed characters to word processor, at least) in order to right what he perceives as the unfair criticism they have received, based on what he has seen and what he knows, then that's fair enough. I have plenty of respect for that, and bearing in mind his reputation was built in the cycling community based on his pursuit of Armstrong that made him seen as something of an anti-doping crusader, nailing his colours to the "Sky=clean" mast knowing that many will see it as selling out takes some cojones.
However, I do have a problem with him insulting his readers' intelligence by justifying that position with arguments so weak they are unbecoming for a journalist of his reputation and standing. The arguments presented in order to justify his belief that Sky are clean are not always but often riddled with holes (the most ridiculous of all being "Froome roomed with one of his teammates, what doper would do that?"), and some of the symbolism is so heavy-handed as to be comical (the worst offenders in that regard have been brought up in this thread a long time ago, like the butterfly moment).
I feel that if Sky are not clean, and Walsh has been kept in the dark, it has been a missed opportunity, whereas if he knows and is in on it then he's dishonest and deserves the stick he's getting.
If Sky are clean, then a great opportunity has still been missed, because the flimsy arguments do not succeed in convincing those that doubt them, and so many questions are left unanswered that Walsh could have answered for us that it does Sky a disservice.