Sir John had been criticised over his insistence on multi-million-pound bonuses for top Xstrata managers.
Xstrata said its independent non-executive directors only intended to recommend unanimously the first resolution.
The shareholder vote follows after Glencore increased how much it would pay for each Xstrata share.
However, Xstrata's independent directors have queried the new bid and are asking for more information.
He points out that Glencore and Xstrata would not be the biggest company of its type.
The list includes Anglo American, Aquila Resources, BHP Billiton, Macarthur Coal, Rio Tinto, Vale, and Xstrata.
Xstrata's shareholders - other than Glencore - would have a 45% stake in the new firm.
The Xstrata finance head will likewise take the senior role in the combined firm.
He is currently a director of Minara as well as Xstrata and UC Rusal.
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Davis and other Xstrata executives are leaving early, and Glasenberg will be the undisputed boss.
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If Anglo's current attempts at restructuring founder, its shareholders may welcome renewed interest from Xstrata.
Xstrata was, after all, born out of coal mining assets spun off from Glencore a decade ago.
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"The strategic rationale for combining Xstrata and Glencore remains highly compelling, " said Xstrata's chief executive Mick Davis.
Analysts said the deal between the two Anglo-Swiss companies would now likely be backed by Xstrata shareholders.
The divestment didn't come as a surprise since Xstrata had until then been focusing on nickel production.
They could buy the thing and sell it afterwards to a private equity company, as Xstrata did.
The output of the other, Falconbridge, complements the coal, copper and zinc businesses of its purchaser, Xstrata.
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Tuesday also brought a deal, with Glencore International agreeing to a long-anticipated merger with mining firm Xstrata.
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Shareholders also opposed the re-appointment of three other Xstrata directors - Con Fauconnier, Peter Hooley, and Ian Strachan.
Shareholders will now vote on whether to accept the offer of 3.05 Glencore shares for every Xstrata share.
Glencore raised its offer to 3.05 of its shares for each Xstrata share, from the 2.8 previously offered.
The deal remains conditional on the support of Xstrata shareholders, some of whom have questioned the revised terms.
China, for example, buys a lot of commodities from Glencore and Xstrata, and may fear prices will rise.
Xstrata chief executive Mick Davis will head up the new firm, with Mr Glasenberg becoming deputy chief executive.
He wants Xstrata to raise its contribution to a social fund from 3% to 30% of pre-tax profits.
Xstrata, whose history is one of serial dealmaking, would doubtless have liked to hang on to the mine.
It came on the request of Xstrata, which has been vehemently opposed to Anglo's merger proposal as it stands.
The board of mining group Xstrata has recommended that shareholders back the merger terms offered by commodities trader Glencore.
To help secure this, there are unconfirmed reports that Glencore has offered to sell part of Xstrata's German operations.
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