The question is older, but I'll answer it anyway.
Twitchio doesn't directly support this.
But you can delete individual messages in Twitch Chat, see the Twitch IRC documentation.
CLEARMSG (Twitch Commands)
You need the message ID for this. You get the ID in the message tags.
Message tags
Code example:
async def event_message(message):
if not message.author.name == self.bot.nick:
message_id = message.tags['id']
await message.channel.send(f"/delete {message_id}")
If you want to timeout someone, do the following:
await message.channel.timeout(message.author.name, 120, f"reason")
Twitchio documentation Channel.timeout