Alleline is the one benefiting most from the Merlin intelligence, as he's the one who takes command of the Circus after Control falls. Yet it is Haydon is "Gerald" and is systematically working behind the scenes in indirect ways for Karla.
So rather than the Shan directly taking control of certain high-ranking members of PISCES and wielding power that way, they might instead choose the senior but not chief people like Haydon, and use office politics to get the most easily-duped (Alleline), ambitious (Bland) or corruptible (Esterhase) into positions of power where they can be more easily manipulated than those already there. And if those people fall from power, it can be misdirected on the KGB and won't come back on the Shan-controlled agents, who remain in place to put another crop of easily-manipulated personnel into senior positions.
And then there's the most evil thing to do: have Smiley being the one who was Shan-controlled all along.
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