Melinda knows the rules. Hell, she only ever joined the Bus because of the rules regarding Agents under suspicion. Those rules were for SHIELD though and that doesn't exist anymore. Most of her wants to respect them but times are hard and stressful and everything she has known for over thirty years has crumbled around her and it isn't the first time. Ward was never within the rules either, yet she knows how that ended. Skye is different though. With Skye, Melinda takes a risk.
She becomes Skye's SO by default but Melinda is determined that if she is going to do the job she will do it right and she will not lose another Agent. Skye was never meant to get as close as she does but it happens in the chaos of SHIELD's collapse. Even Melinda needs someone to lean on and Skye is there, without bias or complications. While Melinda has interacted with her it has never been personal and the way Skye steps up after Ward's betrayal is nothing short of inspiring.
It is worth the risk.
It starts with touches on the wrist after work outs and then smiles after that. From there Melinda hovers longer after taking her to the ground and spends more time in her presence. Skye understand what she means and returns the touches, turns the pins so she is in control and then she kisses Melinda after a mission where no one can see. She says nothing. That says everything.