Agents of SHIELD season 5 will end in May 5, 2018, meaning there will be 4 more episodes left by the time Infinity War hits theaters. So they cannot just kill some of the main characters because they would have to wait for 2019's Avengers 4 for them to return.
AoS showrunners and writers already know for the past few years that they are not getting any support from the movie side, so they already know what's going to happen in Infinity War and have prepared for it. The vanishing will be acknowledged in the show but NONE of the main characters will be among the disappeared.
If they're going to kill off some characters, it's likely going to be the expendable ones like Agent Piper or Agent Davis.