Franklin, 26, looms as potentially the biggest player out of contract at the end of the 2013 season and the superstar will be a restricted free agent with significantly big bargaining powers.
Franklin has already rejected a reported $900,000-a-year offer for up to five more seasons from the Hawks.
The game's biggest scoring power and intimidator is expected to command offers well in excess of the Hawks first bid.
Clarkson accepts Franklin's decision to delay any further negotiations until the end of playing commitments this year is by-product of the league's free agency process.
Free agency was introduced for the first time last October following a full year of uncertainty surrounding just where Collingwood powerhouse forward Travis Cloke would play.
After considering offers well in excess of $1million a year for up to six seasons, the big Magpie stayed at Colllingwood for reportedly considerably less than overtures from numerous other clubs.
"Whether it's Hawthorn, other clubs or the football community, I think we've just got to have to get our heads around free agency and how it's going to impact on clubs," Clarkson said on Melbourne sports specialist radio SEN.
"He's got a contract at our football club for season 2013 and we're going to do everything we can to ensure that that's good for both of us and we'll see what happens at the end of the year.
"But we're hopeful he'll obviously stay and continue to contribute for the Hawks."
Clarkson conceded he could lose his champion scoring source at the d of a potentially disrupted season with on-going conjecture surrounding the future of one of the game's biggest stars.
The 2008 Hawks premiership coach however, remained buoyant that Franklin could yet stay at Hawthorn well beyond this year.
"Staying in one place for nine years is a long period of time now, and that's another thing we've just got to get used to," Clarkson said.
"At some point in time he'll sit down with all the information that's available to him, and I think he just genuinely wants to see how this footy season unfolds before he makes a decision on where he wants to play his footy in 2014."