Personally, I agree that the cost is simply too high to use the current Warp Jammer. 5000 K to unlock, replaces the command center which means a significant economic + other benefit opportunity cost, and it fails to do anything about reinforcements or standard border aggression. This means you still need to neuter all adjacent AI systems, as well as go back regularly to keep them clean. A lot of effort for something with such high costs.
I like chemical_art's idea #3 - Making the Warp Jammer act on it's own and all adjacent human planets (similar to the AI's Interplanetary Munitions Booster). This increase in efficiency makes the cost seem much more worthwhile. Additionally, it becomes a bit more of an awkward tradeoff to use. If you cover all your planets, you've got the dreaded CPA-warp attacks, which is probably worse than the AIP would have been.
Chemical_art's idea #2 is an interesting alternative. Even if the only Warp Jammer improvement was to prevent the current system from putting adjacent AI worlds on alert, this could be a major benefit by reducing the amount of boring cleanup tasks that need to be performed.
I also like, REALLY like, the idea of making it a standalone building. This cuts the opportunity cost of losing the command station, which is a pretty major buff right there.
The concept of the Warp Jammer - an alternative method to allow the player to manipulate the AI's strategic behavior - is lovely. My favorite scenario would be to have the current Warp Jammer as a standalone building, also have a Signal Jammer that prevents the AI from going on alert due the the human planet, and also have an AI Aggrevator that causes the AI to direct all (or most?) waves at a specific planet (could cause waves to come more often, be more powerful, go up a tech level, or even cause a AIP-over-time increase like the Spire Civilians).
Maybe add them to the Zenith Trader?