In the Star Trek: The Next Generation episode "Up The Long Ladder", even though the away team's DNA was taken without permission, wouldn't killing their defenceless clones be an act of murder and against Federation law?
No, because at the point they were terminated they weren't viable. In essence, Riker and Pulaski performed their own abortions. For fictional reasons, they had to show the clones as adults in order to be recognizably Riker and Pulaski, not to mention that showing them younger would raise all sorts of issues. Like it or not, it's more acceptable showing something that looks like an adult being killed than something that looks like a child.
The difference with DS9's "A Man Alone" was that the clone was a fully-functional entity. In essence, the difference was between terminating pregnancy and murdering a baby after it's been born. Historically, and in most cultures, it's recognized there is a difference between those acts.
Starfleet General Order 1 is never fully quoted or recited but is along the lines of "No Starfleet personnel or spacecraft may interfere in any way in the natural development of an alien culture." This would apply if you consider the Mariposans to be an alien culture. In that case leaving any genetic material with the Mariposans would be a direct violation ie: the Enterprise crew would be obligated to kill their clones. However, classifying the Mariposans as an alien culture may be a bit of a stretch as they're a colony of humans presumably originally from Earth. In the case that you consider them to be federation citizens, their use of cloning as a means of propagation would likely be considered a criminal act due to regulations implemented after the Eugenics Wars. This wouldn't necessarily justify the killing of the clones as Starfleet General Order 2 prohibits the taking of intelligent life. It is also stated that Starfleet prohibits the death penalty except in the case of mutiny.
In short, it's a convoluted gray area. There are regulations that allow officers to make extreme decisions in extreme situations and at a formal court martial I'm sure one such regulation could be used to defend Riker. Essentially the killing of the clones would be treated as legal until a flag officer or Federation official called for a court martial.