There is no way for Riot to protect people in a non LAN environment(aka at thier homes). It is a sad truth of the matter. Part of the problem is that Riot can not know if a team is telling the truth.
Things Riot can do.
1 Disable the pause game feature. Should the pause limit be in place when in LCS games it is disabled? Obvious answer is No. LCS teams are given as long as it takes to get the problem fixed. Though their is a whole team of people to fix any problems that come up. People in a non lan eviorment should have the time need to go to a new location (friend/family) and get back in the game.
2 Montioring software. Some FPS tournaments actually run their own back round software to verify legit play. This software would allow riot to see if a connection issue is actually happening. Alot of clever things can be done with this type of software.
3 Tournament realm. All games are play on it i believe. Roit needs to force higher protections. Random people should not be able to get IPs off of it. The lack of beefed up security for this realm is sad. This realm should be more than just a private.
Things teams can do.
So here is a sad truth. Teams are not doing everything in their power to prevent DDOS.
1 They should not be using skype in pro matches. Lets forget the latency issue that Skype has and focus on the fact it is not a private server. IF teams would spend the 15 bucks a year for a private server voip it would be harder to trace players. Their are so many server compaines that run voips that knowing which in is almost impossible. Plus they are so cheap for a 10 slot unit that you could have 2 different companies to have a back up if one went down. Obviously teams would have to keep their mouth shut on what they are using.
2 Teams need to plan ahead and try and be at another location that they never use. This one is hard, but would do so much. Being able to go to someone elses house or even talking to the internet company and forcing a IP change in advance would make it harder to DDOS. Most people do the research on peoples IPs days in advance. These cahnges make that research useless.