So, I should believe that Prof David Nutt was right and Alan Johnson was wrong (both in the reclassification of cannabis, although that took place under his unlamented predecessor, and in the sacking of Nutt)? Well, much as Prof Nutt's science is probably correct and a Nu-Labour Minister (any) is probably hideously and authoritarianly statist in their utter wrongness, no, not necessarily.
Cannabis is, and remains, an illegal drug. The classification of the drug within that system is driven partly by scientific concerns (seriousness of the impact of the drug and of its harm) but also by political concerns (harm to society, policing and sentencing policy). The latter clearly involves electoral political issues - it is perfectly reasonable to have one party slavishly following the drugs = evil line (inconsistencies with alcohol and tobacco policy slowly being eradicated thanks, or not, to the BMA and govt-funded 'pressure groups'), one taking a libertarian line (about the only liberal thing about the Liberal Democrats), and one completely at sea between its traditional roots and the 1960s/70s dope smoking past of its current front-benchers. And it isn't unreasonable on the "experts advise, ministers decide" principle to require that advice to ministers is private.
The current government are both eager to publish and rely on any 'scientific' advice, however flawed (see informed commentary on the Poppy Project's 'Big Brothel' report here and here) whenever it matches their 'political' objectives but they also published the actual Advisory Committee report! That they, politically, disagreed with. So what we have here is a politician being surprised that a scientist has stood by their researched and published opinion, rather than changed their mind to the politician's whim. So yes, Nutt right, Johnson wrong. Pandering to the popular prejudice. But because of hypocrisy and "policy based evidence making"* - not some mystical right for science to over-ride politics, so it need not always be that way.
Edited to clarify - so Johnson isn't wrong to weigh the scientific advice and discard it in favour of political concerns - he is wrong for sacking an independent advisor for continuing to stick by a published-by-the-government report. Nutt isn't (necessarily - I certainly don't have the knowledge or the access to data to dispute the committee's findings) right about cannabis or ecstasy, he is right for stating the prevailing view of the committee in the report and for sticking by it when the politicians decided other considerations were more important.
* - This is an older term than you might think, given its rapid re-adoption for this subject. However it was invented to describe nu-Labour.