I'm a big fan of the changes, personally.
You can still prevent spread with inquisitors, but they don't simply stonewall other religions like they used to. They also work against passive spread now, so Orthodoxy doesn't just ignore inquisitors anymore. Now you can still make a determined effort to convert someone, and now you pay more than just 200
for an inquisitor action; you pay in
unhappiness and all yield outputs per turn. Now missionary actions can paralyze a foreign civ's economy, if they are determined to preserve their religion. This threat means we now have an actual basis for "wars of religion", because you can always just declare war and capture all their missionaries and force another civ to back off the old-fashioned way. It also means that pushing your religion on another civ, and the thousands of
faith spent on doing that, might actually yield some returns, rather than a single inquisitor wiping out all your missionary spread investment.
There's a lot more decisions and interesting trade-offs to accepting/fighting a foreign religion's influence on your civ now.