At the time, and this is often missed, there wasn't really a coherent policy for how to deal with slaves. There were forwards and backwards steps taking place. Similarly there wasn't really a coherent policy on how to deal with the inhabitants of the seceding states - were they enemy combatants, or were they legally speaking citizens of the US? Or both? How was such a thing to be handled? There was no coherent answer.
McClellan had earlier sought (and got) permission to share his views on military affairs, and the subjects he touches on in the letter do indeed touch on military affairs; he's arguing for there to be a policy.
Remember, as of the Harrisons Landing letter McClellan is the ranking officer of the US Army. If he is not allowed to suggest to the President his private opinions on policies that are related to the military sphere of affairs, nobody is - and I don't think that's really fair.
MacArthur, for his part, publicly criticized the Administration - something that McClellan didn't do. The Harrisons Landing letter was handed to Lincoln in person, and privately - in keeping with Lincoln's wishes for secrecy.