But Kidney still expects Sexton to be a fundamental part of his Ireland side, even if he is not based in the Emerald Isle.
"Jonny would be a very proud Irishman, Leinsterman, St Mary's man and I don't think that's ever going to change," Kidney told the Irish Examiner.
"He's playing for Ireland as long as he's maintaining the standards he's been playing at and I'd see him being able to develop even more because he's probably just coming into his prime and I shouldn't see that that should affect his international career.
"It will put a bit more pressure on travelling and access to him and will open the door to other fellas to showcase themselves at home as well.
"We live in a professional age, everybody has to make decisions, the players, IRFU, clubs, provinces, and I respect that. That's the age we live in."
Meanwhile, Ulster wing Andrew Trimble has been omitted from Ireland's 33-man training squad for their opening match with Wales on Saturday.
Trimble, who has 49 caps for Ireland, featured in the Wolfhounds' defeat to England Saxons on Friday but he has been overlooked by Kidney, seemingly at the expense of provincial teammate Craig Gilroy.
Kidney is due to name his 23-man matchday squad on Tuesday.
Ireland training squad:
Michael Bent, Rory Best, Tom Court, Sean Cronin, Gordon D'Arcy, Keith Earls, Luke Fitzgerald, Declan Fitzpatrick, Craig Gilroy, Cian Healy, Jamie Heaslip, Iain Henderson, Chris Henry, Paddy Jackson, Rob Kearney, David Kilcoyne, Conor Murray, Mike McCarthy, Kevin McLaughlin, Fergus McFadden, Dave McSharry, Sean O'Brien, Donncha O'Callaghan, Brian O'Driscoll, Ronan O'Gara, Peter O'Mahony, Eoin Reddan, Mike Ross, Donnacha Ryan, Jonathan Sexton, Mike Sherry, Devin Toner, Simon Zebo