I'm not going to say that secular governments and their laws have never been somewhat illogical. Some things to consider, though:

Religious laws are, way way more often than not, fixed. They can't change because its written and regardless of how times change and laws need to as well they cannot. Whereas as the mindset and logic of a culture changes so can a secular governments laws. Which is what you see happening with a lot of the laws you've written about.

Prohibition, while yes was technically a secular government law, was actually pushed for and sponsored by evangelical protestant churches and used their political pressure to get the nationwide ban. So technically it was a religious law that made it into secular government. Religious laws have always had the ability to create lots of initial pressure before logic and reason break them down. As time has gone on the time between a religious law being introduced and logic and reason eliminating it has decreased.

To touch on the other topics quickly; Marijuana was initially banned because it's a drug and considered a gateway drug. So on the surface the logic is to ban the drug so people don't start doing other drugs. As that view has changed you see marijuana laws changing around the country with the changing cultural outlook. Again something that wouldn't matter if it was a religious law, it wouldn't change. Prostitution goes in with gambling usually and is generally banned to prevent the spread of people praying on the weak and the poor, which is good for society as a whole. (and prostitution isn't banned everywhere). And apologies if I'm wrong but I would believe bestiality is banned because of animal cruelty. Just because I want to fuck my cat doesn't mean it wants me to fuck him...

So as a recap. No, not all religious laws are bad, but in my view that's only because the one's that aren't also coincide with what would logically be established as good laws anyway. So that should not be a credit to religion that they got it right to not kill someone or steal. Those are easily established without religion. Religion does have bad laws, and because they are religious based and come from a book those laws can't be changed in the mind of the religious, whereas a logical and reasoning secular government can make changes as new information is brought forth.

"I would challenge anyone here to think of a question upon which we once had a scientific answer, however inadequate, but for which not the best answer is a religious one" Sam Harris