Bruhn, a Geelong local who was GWS' pick No.12 in the 2020 draft, is poised to request a long-expected trade to his home town.
The standard AFL draftee contract is two years and Bruhn's departure would follow Jye Caldwell heading to Essendon two years ago.
"Obviously it's disappointing," McCartney told AFL Trade Radio.
"Tanner's a wonderful young man and invested really heavily in our football club.
"He's played 30 games over the last two years and there's probably not many from that compromised draft in the COVID years that have played that many games.
"It is disappointing. It's a reality. We'll just have work with it now. It looks like it's leaning that way with Geelong and we'll sit down with (Cats list boss) Andrew Mackie and thrash out what we can get done there.
"But two years, that is really disappointing.
"We make no bones about it. We'd love to see our early draft picks at least being a minimum three years because two years can drift pretty quickly."
McCartney said player salary demands tended to explode in their third year which meant clubs paid a premium just to retain them, regardless of whether they were performing.
He noted Caldwell and Bruhn would both have left after COVID-19 affected seasons which meant they'd barely been in Sydney for large chunks of their contracts.
McCartney acknowledged there would need to be a cut-off point in the draft for longer contracts, while deals would need mechanisms to protect players.
GWS are eyeing a monster draft haul through trading Bruhn and Richmond-bound pair Tim Taranto and Jacob Hopper.
"Tim's a bit different to Jacob because Jacob is in contract," McCartney said.
"Blair Hartley and the Richmond guy, they understand the quality of these players and they understand it's going to take a little bit of work with one still in contract. We'll keep working through that."
McCartney expected forward Bobby Hill's switch to Collingwood to be a straightforward affair early in the trade period.
Elsewhere, Western Bulldogs veteran Jason Johannisen has signed a new two-year deal.
Johannisen, 29, was linked to Gold Coast as an unrestricted free agent.
He has kicked 70 goals in 176 games and won the Norm Smith medal in the Bulldogs' breakthrough 2016 grand final triumph.
Brisbane have delisted Lithuanian-born Irish category B rookie Deividas Uosis, 2018 first-round draft pick Ely Smith and pre-season pick Mitchell Cox, none of whom made their AFL debuts.
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