I'm not sure it's right to characterise the Talisman as an end-game tech. It takes a few research levels to reach, but it's not that expensive, and you can get there relatively quickly if you focus on it. And who says the intermediate levels aren't useful? Shrines are great!

You can for example save a lot of research points by getting DUCs and PDCs and then ignoring all other weapons development. With Talismans, ECM and armour, they're the only weapons you need to make some pretty dangerous ships.

How to counter them?

Long range weapons and max-range tactics, so you are shooting and religion-boy isn't.

Otherwise (as others have already said) maximising your to-hit chances and getting as close as possible, reducing his advantage to a minimum.

The point about play-balance is that he spent 1500 points to get religion. What did you spend yours on? Better Intel ought to let you sabotage his engines or steal his ships. Better production would let you outnumber him. Better research would give you more damaging weapons - he may be hitting more often, but when you hit, it hurts a lot more. Etc.

Mark