Actress Ming-na Wen spoke about the emotional state her character was in at the end of season two of Agents of S.H.I.E.L.D. (spoilers ahead):
"In any situation when someone is so devoted to their work as May was, but then realizing over the last two years that S.H.I.E.L.D. isn't really what she dedicated her life to. That there was definitely a lot of corruption to S.H.I.E.L.D., as well as uncertainty now with the Inhumans being brought in by Coulson. It's going to be figuring out her final decision in Season 3 and I think Andrew will probably play a part in it."
She's referring to Agent May's ex-husband, who we saw offering counseling to Skye, which might be a precursor to working with the Inhumans later on.
Where would this leave the characters?
Agent May was a wonderful mentor to Skye, and seeing their relationship develop onscreen was amazing. It would be a shame to see that relationship end because of the direction S.H.I.E.L.D. is taking. That being said, I think Coulson's leadership has actually been questionable. While I don't think that Gonzales and the others did the right thing by covertly spying on Coulson, I also don't think they were wrong in being concerned about Coulson's decisions. Agent May was one of the few people that seemed to be trying to do right by everyone, and Coulson actually respected her judgement. With her gone, will Coulson be willing to listen to anyone else?
That being said, this could all be set up for a tie-in with Captain America: Civil War, set to be released next May. Season 3 will air in September, but it will most likely be split up like it was last season, with the last episodes airing next spring. The show alluded to Winter Solder and Age of Ultron, so it would make sense for Marvel to use the show to create hype for their next big release.
That's really all we want to know!
An assurance that May will continue to be an integral part of the show, and that her character will continue to develop, is really all fans need right now. Where would the show be without her?