While I haven't yet studied the ack filtering code in depth, Ryan indicated that some of those concerns were considered in its design.
In particular, it won't ever delete the last remaining ack in a flow's queue, only replace it with a more recently arrived one. That should take care of interactive performance, which has always been high on Cake's design considerations. Cake itself is also careful to not drop the last packet (of any type) in a flow's queue, for similar reasons. - Jonathan Morton
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