When you hear Skye exiting Stealth, quickly find her and shoot her with Disengage. This will reduce her damage a lot since she'll be further away.

Using Nimble as an Item is good against Cassie. The player will have to review his/her shots trajectory to make sure to hit you with your different movement speed.

In the start of a round, go near the objective but stay behind and wait for around 5 seconds, then use Scout to determine which way Skye will flank. This also directly counters Stealth.