They have attached the TV series to the Movies extremely well, not to mention have had characters and races (Inhumans) in there as well to say "it's all connected". They should NOT change anything they're doing. The time line is pretty clear as it goes along. Agent Carter takes place after First Avenger, telling the start of S.H.E.I.L.D. and where Peggy was afterwards. Agents of S.H.I.E.L.D literally crossed over with EVERY Phase 2 movie ( - Guardians) mainly Captain America 2 revolving around Hydra in S.H.I.E.L.D. Daredevil....... only mentions characters and 2 big battles of Phase one...... If they make it differ from the MCU it wouldn't make sense.