Short answer: no.
Long answer: pillar's restriction means that the mana can only be used to pay the casting cost of a multicolored spell (such as replicate). Paying for the Isochron scepter ability, although it will ultimately be used to cast a multicolored spell, is not paying the mana cost of a multicolored spell.
But "replicate" is an activated ability, such as the copy from scepter. The main difference between both abilities is the source, which is an artifact (colorless) or an instant (multicolor), however, the source should not matter but the text of the effect. If you activate isochron's ability, it casts a copy of a multicolored spell (the imprinted card), if you activate replicate, it casts a copy of a multicolored spell. (Bare in mind that Isochron scepter text from mirrodin says "You may copy the imprinted instant card and play the copy without paying its mana cost.". And paruns text "Add one mana of any color to your mana pool. Spend this mana only to play a multicolored spell." It should be legal, because the source should not matter. For instance, devoid cards cannot be paid with pillar, not due to the source (multicolored mana) but to the spell (colorless).
To be technical, replicate is a triggered ability which triggers the ability to allow you to pay additional costs.
702.55a Replicate is a keyword that represents two abilities. The first is a static ability that functions while the spell with replicate is on the stack. The second is a triggered ability that functions while the spell with replicate is on the stack. “Replicate [cost]” means “As an additional cost to cast this spell, you may pay [cost] any number of times” and “When you cast this spell, if a replicate cost was paid for it, copy it for each time its replicate cost was paid. If the spell has any targets, you may choose new targets for any of the copies.” Paying a spell’s replicate cost follows the rules for paying additional costs in rules 601.2b and 601.2f–h.
You're not paying for the triggered ability. Rather, the triggered ability is triggering and allowing you to pay additional.
Isochron, on the other hand, is an activated ability. You pay 2 of anything to activate the ability of isochron, the activated ability then casts the spell.