It enables control of traffic in the sea, Rivain hasn't been confirmed to have an access point to the deeproads and even if they had one, it likely will be so infested with Darkspawn it would be impassable, Lyrium trade is vital to both sides of the conflict and through Rivain they likely could control it fairly well if they so desired. Individual mages certainly, but it prevents things from escalating further inland if things go bad in the South, That's my view of it the control of the sea will likely prevent random seaborne invasion, That's my point if, things actually do come down to individual armies clashing, rather then mass skirmishes across the continent.
It wouldn't be over much advantage in counter insurgency and thus its importance likely will not be over relevant to the Plot, its just i look through the eyes of a military tactician and cannot help but see the advantage here, preventing Lyrium traffic to former circle mages, corralling the North and having a steady logistical and access point to both North and South would be invaluable to any war effort.
Although I agree that having dealt with the Rivaini mages is a good strategic advantage for the Seekers-Templars, I don't think it is in the way you are thinking.
Access to the sea is good for their mobility, but not to the control of the trade routes. They can't, they don't have the means or the manpower. Those waters infested with pirates from the Felicisima Armada who, as Sir JK has pointed out, wouldn't want some skirts trying to break their trade and has enough manpower to face the Qunari fleet. Also, the other only important magic centers in the north are Antiva (just a city, can be overlooked), Anderfels (too dangerous and with the danger of pissing off the Grey Wardens) and Tevinter (no, just...no), so the Templars don't gain anything by trying to control the north.
BUT with Rivain controlled, they can send those extra Seekers and Templars to the south, to reinforce their brethren, so yeah, it is an advantage. They will probably try to take some keeps for themselves, to have lands > food & money for the war effort. Of course, then some strange human/elf/dwar/qunari will appear wearing a very ominous symbol that looks eerily similar to the Seekers' and Templars' and say: "Nice castle. I'll take it".
I agree with wcholcombe, the mages can't win using conventional warfare. So that means diplomacy, unconventional warfare or some mages doing a very stupid thing to win that can cause the end of the world or something.