Response to an unknown guest
The situation with the Transformers seems very likely. Atlas will definitely want to study their resources for their military, and RWBY will definitely help them.
Response to another unknown guest
Yeah, the 501st would probably go with Winter's and RWBY's plan. That is, if they were fed up with Ironwood and the Ace-Ops (and they reached a breaking point like killing their own men). They would definitely execute him if he betrayed them. I'm not sure about what they would do with Emerald or what Fives would think of Penny. I do like human Penny, but I'm not sure if Fives would have much of an opinion.
As for the speech, while it hit close to home for the clones, the Ace-Ops is a different story. I could see Elm have second doubts, Vine would take a moment to think about what has happened and what will happen, while Harriet would flat out kill them.