Does damage from a source with wither use -1/-1 counters even if the source also has deathtouch?

Wither (CR 702.79) causes all damage that source deals to creatures to be dealt as -1/-1 counters instead of regular damage. This replacement effect applies whenever the source deals damage to a creature, period — it does not interact with or depend on deathtouch.

Deathtouch (CR 702.2) is a separate ability stating that any amount of damage that source deals to a creature is enough to destroy it. It does not change how damage is marked; it only affects the threshold for lethal damage.

When a source has both abilities, wither's replacement effect still fires, so damage is still dealt as -1/-1 counters (CR 702.79a). Deathtouch then still applies — since even 1 damage (placed as a -1/-1 counter) from a deathtouch source is considered lethal, the creature will be destroyed at end-of-combat state-based actions (CR 704.5g), and the -1/-1 counter also remains on the creature.

Example: Your 2/2 creature with both wither and deathtouch deals 1 damage to an opponent's 4/4. That 1 damage is replaced by a -1/-1 counter (wither), making it a 3/3. Because the source had deathtouch, that 1 damage is considered lethal (CR 702.2b), so state-based actions destroy the 4/4. The -1/-1 counter placement and the deathtouch lethality both apply simultaneously.

So yes — wither always converts damage to -1/-1 counters on creatures, and having deathtouch on the same source does not suppress or override that. Both abilities function independently.