I don't follow this line of argument, since both games have similar missionaries and city conversion mechanics, and that is the limit of interaction that IV provides. If you are talking only about religion, I don't see how you could credibly argue with the assertion that V is much more layered than IV.
(Disclaimer: small wall of hastily written text). Also, I am going to assume that's a typo you wrote, as:
I am making the argument that religion Civ 4 is just as, if not more so, interactive with the other systems in the game than in Civ 5.
These systems include, but are not limited to: diplomacy (big one), happiness, yields, and one's military (or the lack thereof), and are, broadly speaking, implemented by
beliefs, the piety tree, and making the AI hate you more if you even dare try converting one of their cities, and the world congress world religion proposal in Civ 5, and
civics, apostolic palace, and diplomatic benefits/penalties and interactions (i.e. Isabella demanding you convert to Hinduism....) in Civ 4.
The missionaries are anything but similar. City conversion mechanics are different enough that you cannot really lump the 2 together as "similar". And of course I am not only talking about religion in the strict sense of "does this city have a religion" or not - that would be entirely pointless, as the religion system is tied in different ways to the different systems of the game.
In Civ 5, missionaries are purchased (only) by faith, as opposed to Civ 4 which must be hard-built by hammers/production. This by itself forces a significant choice upon the player: "Can I afford to forgo the production of units/buildings for this missionary?". In Civ 5, this area of decision making has been stripped/watered down - the opportunity cost is far less punishing, as you can only purchase belief-specific buildings (or units, if you have Holy Warriors/Religious Fervor), or save up for a great prophet using faith.
You no longer need to care about whether you're going to be overrun by Barbarians or Shaka/Montezuma's army by your doorstep when deciding whether or not to invest hammers into your missionary, as Firaxis has kindly divorced the 2 altogether for you so you do not need to make that decision, you need only worry about whether/when you can afford the next cathedral/mosque/university/great prophet in the majority of games (exceptions would be Holy Warriors and Religous Fervor beliefs).
City conversion in Civ 5 depends on the conversion of citizens, with the city "following" the religion that has converted 50+1% of the citizens in the city, and you can purge religions with the use of Great Prophets and Inquisitors.
City conversion in Civ 4 however, has the "missionary fail" mechanic, which works by applying a %chance failure to the missionary (which is single use) if there is/are more than 1 religion already present in the city. One can have multiple religions in the city (which is great as the Free Religion civic is very powerful lategame), but can block the spread of
non-state religion spread with the civic Theocracy.
There is no automatic spread beyond the automatic spreading of the first religion into a city: i.e. a city with Christianity already present will not convert or gain the religion Islam, even if you spam 10 cities next to it with the religion Islam present.
In Civ 5, the AI will only care about what you do with your religion if you even dare to convert a single city of theirs to your pagan beliefs. They'll hate you a bit more if you refuse to stop after asking. If you both have the same religion in the majority of your cities (and the AI has not yet founded a religion yet)? Congratulations, you have now a -5/-3 diplomatic bonus (negative modifiers = like you more, positive modifiers = hate you more, by the way in case you were wondering about the scale in Civ 5), which is about the same as accepting an embassy in your capital. And we all know how much that helps in getting the AI to like you.
In Civ 4, the AI has the potential to both like or hate you depending on your religious affiliation, with these bonuses/penalties accruing over time, so you cannot simply jump from religion to religion every time someone asks you to convert and keep the same diplo bonuses with your old friends. One thing to note here, is that the AI in Civ 4 is much, much more willing to declare war if they don't like you enough, and religion plays a very big part in defining the cliques present in the world (i.e. who is going to be willing to tech-trade/broker with you) - anyone remember Civ4's Isabella..?
And finally, as you mentioned before, we can start a whole new discussion on the concept, effects, and the gameplay decisions that go into the Social Policy Tree (Piety) and the Civics (religion), as well as the Apostolic Palace and the Shenanigans you can pull with it.