I move to uncontested Forbidding Waste with my irresistible Faefolk. I charm enemy Sonya into it. Who gets the -2?

The -2 penalty applies to Sona. She's the defender and she's defending alone.

Here's the sequence:

1. You move Irresistible Faefolk to the uncontested Forbidding Waste. Because you applied Contested first, you are the attacker (per FAQ #11223, Rule 459.2.b.1).
2. Faefolk's trigger resolves and moves the enemy Sona to that same battlefield. She becomes the defender.
3. Forbidding Waste checks: "While a unit here is defending alone, it has -2 [S]. (It's alone if there are no other friendly units here.)"
4. Sona is the only unit her controller has at that battlefield — Irresistible Faefolk is an enemy unit, not a friendly one. So Sona is defending alone, and the -2 [S] penalty applies to her.

Irresistible Faefolk is the attacker, so it never checks "defending alone" — it's unaffected. If you later moved a second friendly unit alongside Sona, the penalty would immediately cease (FAQ #10921).