In response, my opponent casts Horribly Awry. Can Horribly Awry counter my Sylvan Messenger?
Yes, Horribly Awry will still counter your Sylvan Messenger. (And so to answer the title question, no you can't raise the CMC of a spell.) Geist-Fueled Scarecrow adds an additional cost, but this doesn't affect either the mana cost or the converted mana cost of the spell:
202.4. Any additional cost listed in an object’s rules text or imposed by an effect isn’t part of the mana cost. (See rule 601, “Casting Spells.”) Such costs are paid at the same time as the spell’s other costs.