For DoS traffic, it'd be nice to have some agreed upon rate limit rules of obvious syn flood and similar traffic which both stop the attacks, or slow them down so they don't affect anything and cause complaints, while still allowing legitimate traffic to flow as normal. Scaleway knows about Tor, but they are also operating out of France and have stricter legal requirements to follow - it's understandable they want a rapid response to any complaints.
My advice for dealing with future complaints...
1) Respond explaining the traffic is coming from the Tor network and you can't stop entirely but you can stop the traffic from coming from your exit.
2) Block outgoing traffic to the affected IP with your exit policy, if it's an attack directed towards a website I'd go through DNS Records and block all related IP Addresses. Perhaps the affected /24 or /16, better safe than losing out on 100Mbps so of bandwidth or from the Tor network :)
3) BE FAST: Scaleway isn't playing games anymore when it comes to managing abuse. They're allowing Tor Exits, but only if you are very fast about managing abuse. If you get to the point where they say next complaint and they suspend your service - stop running an exit node and operate in relay only mode. Exit bandwidth is important, BUT, unique guards controlled by a variety of people are still necessary. It's something to consider if you've damaged your relationship with Scaleway beyond repair.
4) Maybe only allow DNS, HTTP, and HTTPS ports. That's less port choice for sending out a syn flood and makes you less likely to get a complaint.
Cordially,
Nathaniel