Which would be a more effective border defense for the southern Riverlands: a series of major castles that would require storm or siege to prevent attacks on the rear of an invading army… or a more closely space series of signal towers meant to warn Harrenhal and Riverrun but unable to mount a major resistance themselves?

The former, clearly. Far better to have a defense that can slow or halt the enemy than a defense that can’t. 

Although honestly, I think a lot of the Riverlands’ problems on its southern could be solved with a riverrine navy on the Blackwater Rush (which the Iron Throne would probably have a problem with) that could contest fords, along with the improved fortification of Stony Sept, and (surprise surprise, it’s me) a canal linking the Red Fork to the Rush (allowing for good interior lines between the two halves of the Riverlands).