it would seem that some of this lies in the status of the south at the time that he called for conscription. according wikipedia, he can call up troops “whenever the United States shall be invaded, or be in imminent danger of invasion from any foreign nation or Indian tribe.” or “whenever the laws of the United States shall be opposed or the execution thereof obstructed, in any state, by combinations too powerful to be suppressed by the ordinary course of judicial proceedings, or by the powers vested in the marshals by this act”.
Once the south seceded, which was perfectly legal, they were their own country. Thus, he could only have sent troops into the south if they were threatening invasion of the north, since, in regards to the second provision, they were no longer states subject to federal laws.
As far as whether those acts legalize conscription in the first place, I am unsure in the wording.