Rajarata was abundant due to regular wars for the Rajarata land. Sinhalese kings tried to re established Rajarata, but they weren't allowed by Pandyan empire. They had full control of the Sri Lanka in 1450. They got real opportunity after 235 years from the Tamil invasion. That time people adjusted to wet zone so it is possible that descendants of the engineering families didn't had the practical knowledge to rebuild the dry zone hydraulic system. It wasn't that much simple. Even British couldn't understand how the system works. 
So clear major reason is they were adjusted to a another system. Also non existence of expert knowledge to rebuild the system could help to not to go to dry zone again.  But clearly it is not enviornmental issues. It was run more than 15 centuries.
I don't see Magha is irrelavant here. Magha doesn't mean only Magha. He couldn't do all the things alone. He was supported by his army.
Even king didn't had child army had children. Those are the people who came to Jaffna.   

 pre History of Jaffna kingdom 

Jaffna was part of Rajarata before the collapse of Rajarata. Some people trying to say there was independent kingdom (convergence) Jaffna. But how there can be a kingdom without people ? People came with Magha's army. So due to what it could survive from the power of Rajarata ?   

 Starting point of Rajarata 
Magha is not the one who established Jaffna kingdom. Magha is the last king of Rajarata. People accept Magha as king as they couldn't find any royal blood at that time and Magha was Nissanka Malla relative. Also sinhalese power was very weak at that time due to regular providing of strong armies to assist Pandyan to servile from Cholas. Due to this Veera Pandyan a Pandyan prince who get help from Sinhalese and couldn't servive chola powers invaded weak (unstable due to internal conflicts for kingship) Pollonnaruwa. Then Kalinga Magha (Sinha) invaded Rajarata with army of Tamils. There was a battle Magha defeated Veera Pandyan. Magha was accepted as the king. But it wasn't sure whether Magha was controlled by his army chiefs. Armies destroyed Buddhist stupas (may be to find treasures). Also there wasn't way to feed large number of army. Therefore they expelled Sinhalese from north.
People go against the king (as they did to Mahasen) and fight against king. Magha had to abandon the Rajarata. This army wasn't big as previous chola armies. Previous occasions Rajarata rulers completely expelled previous chola invaders and those who wished to join  king was also allowed ( vellakkara group). But Magha's army had good support from Pandyan (It is not clear why Pandyan betrayed Sinhalese as Sinhalese regularly provided armies to survive from Cholas). Pandyan was just near Jaffna and able to respond very quickly. After repulse of Sinhalese Magha's descenders had to accept they obey Pandyan King. Pandyan ruled/assist jaffna with military family called as Aryachakravarthi. But in 1323 powerful Muslim empire destroyed Pandyan capital and captured the king. After Pandyan was ruled by Muslims. They didn't care to assist Jaffna. At this point Aryachkravarthi him self made as the king of Jaffna. 
It is not right to say Magha as the establisher of Jaffna kingdom. He was the king of Pollonnaruwa but after his death and tamil forces was expelled from Rajarata core areas to Jaffna they were under protection of the Pandyan king. So Arachakravarthi established the Jaffna Kingdom