You are describing a sound tactic
(in the game and in the real world)
It has been said that the goal of military action is to take a fair fight, and make it unfair. Most of martial history, from drone strikes to throwing rocks from a high place, has been about giving yourself an advantage. And this is no different.
In the real world, when firing from behind cover, people often drop behind it completely to reload, or between shots. They see no need to expose their body to attack at all times, and instead choose to only become vulnerable when they intend to fire. You can think of this as similar to what your Rogue is doing: they expose themselves to danger when they need to, and otherwise stay prone.
And to claims that this is "cheese," keep in mind that this is tactically similar to using a Rogue's Cunning Action to Hide each round, and can be countered by most things that counter that (Medix2 gives some great examples , like having enemies Ready an action to attack the Rogue when exposed, or doing something that gives Disadvantage to the Rogue's attacks to rob them of Sneak Attack damage). Also, this tactic is not entirely without cost, because going prone every round has some inherent drawbacks.
What you give up doing this
There are two major things you lose with this tactic
1.) You are vulnerable to melee attacks while prone.
If you can get on the roof, then odds are good someone else can too. And as you stated, while a creature is prone (PHB, p. 292):
An attack roll against the creature has advantage if the attacker is within 5 feet of the creature
The higher up or less accessible the roof you're on, the less this is an issue. But you never know when an enemy might summon an ally, or unexpectedly cast the Fly spell, or quietly climb the wall. If you find yourself in melee range while prone, enemies will get advantage on their attacks.
Besides the mechanical vulnerability, you are also likely cut off from your allies. If your rooftop is hard to access, keep in mind that your close-range friends may have trouble coming to your aide. And you'd have some trouble reaching them as well, which brings me to my next point.
2.) You lose some mobility
Your strategy ensures that you lose half your standard movement every turn standing up. This could cause a problem if you need to move far in one round. Combat is dynamic: an enemy may move around the battlefield, perhaps moving out of your range, or into a place that has total cover from your vantage point. If this happens, you may not be able to keep up with them. Your cunning-action Dash makes this less of a problem, but you'll not only have to spend movement to stand up, but also to get down from the top of the roof.
Essentially, the more inaccessible you are, the safer you become, but the harder it is for you to adapt to enemy tactics. That being said, there are a lot of situations where going prone defensively then standing offensively is a great tactic! If you think it will help in your situation, I say "go for it."