In fact, all of the same reasons apply to Armin: Annie's mission should outweigh any personal feelings. In the situation with Marco, it was not just some initiation killing, or fear of Reiner's threats, but the elimination of a potentially dangerous witness (what he still did not understand/accept/realize what he heard does not make him less threatening to them). Yes, Annie did not want to take part in this. Yes it was a test (the test of her preparedness to go to the end).
But, as I say before, all this applies to Armin as well. Only in the case of Marco, Reiner and Bertold could have “fixed” their mistake themselves, without Annie’s participation (but as we all know, they forced her as part of the test. Because both understood that Annie was not feel much loyalty to Marley or to the mission). And in the case of Armin, all this is only Annie's decision (and her own mistake, which she did not want/could not "fix").
All three shifters were aware that Armin could become a bigger threat (which he later did). And the situation prevailing during the 57th expedition (and Annie's more than notbl actions in relation of Armin) essentially made this one hundred percent outcome. And still she chose not to kill him (more than once).
The fact that Reiner did not stand right behind her shoulder then did not mean that he would not carry out his threat. Reiner is crazy but not a fool. And Annie knew that. Although with an increase in her chances of revealing her cover, Reiner's threats have become less relevant...
And about Marco's death: it was not a comparison. Because Armin was not killed.
But Annie had a chance to just crush him. One hit of the foot and the problem is solved. And it would be a much quicker death, than the one that Marco received. She didn’t even need to know who it was. Because she had enough evidence that this was not Eren: she got a good look at Armin before he had covered by hood after falling from the horse. And she probably picked up something from the shouts between senior officers: they didn’t particularly conceal negotiations among themselves, not realizing that Female Titan was reasonable... Damn, bad tempered Eren would have attacked her for killing his team - a fact confirmed by canon. And Annie, all of the 104th, knows that.
As you can see, there is nothing complicated in my reasoning (although it is possible that I incorrectly express my own thoughts - English is not my native language).
I do not exclude the possibility that she allowed herself to spare Armin, because she was sure that she would be able to capture Eren and finally end the disguise.
And when Armin came to her in Stohess, Annie already knew what she was uncovered. She could have killed him and used her knowledge of the city to hide and try to escape (no one would have come to his aid without a signal). Considering that then she already abandoned the mission and just wanted to return home, she missed a great chance.