In most universities in Australia, a student normally takes 4 courses per semester, and a language course takes up one of those slots. So a language stream through university is 1/4 of the load, perhaps with some double courses here and there. If you were in a classics major, you'd round that out with extra literature courses, some ancient history, and so on.
Seminaries are a slightly different kettle of fish. Those modelled on universities have to slot languages into the same kind of structure, and so are far less likely to hold a stream of language right through, unless from the 2nd year on they simply integrate it into biblical-exegesis classes.
Back to universities for the time being. Fairly standard for an Arts subject is 3 hours contact time, to be matched nominally (but rarely) by 9 hours of private study. This is the basis for how I'd revise a languages program.
Raise your contact hours to 10.
If comprehensible input is going to be the main driving force of your language acquisition, you need to do everything possible to maximise that input, and raising the contact hours is the first step. It's what's going to let you actually communicate and engage with the language, rather than memorising paradigms at home and doing translation exercises.
So, argue that your languages course should be more like a Science course with labs and pracs and so on, and far less like an Arts course where you can lecture some content and assign some reading.
How are those 10 hours a week going to be filled?
Firstly, the main teacher should pick a text, or write their own, that is going to be adaptable to a communicative model. In Latin, there's no substitute for Oerberg's Lingua Latina. I'd make it the basis of my classes and syllabus. Teach through TPR and TPRS and work through the text, always in Latin.
Secondly, assign reading-labs. Gather a significant amount of graded Latin reading and require students to work through them in their own time, but not as homework. Maybe use nodictionaries.com or something. The idea is that students should spend two hours or so a week simply reading Latin extensively, without seeking to translate.
Thirdly, employ your second year and third year students to run conversational classes. These should build off the readings and the text/main classes, and look and feel like a modern languages class. Students can be discussing everyday life, a topic, the reading for the week, etc.. In terms of getting 2nd/3rd year students to run them, I'd just block that in as a requirement and part of the hours for the 2nd/3rd year subjects. It will certainly help them develop more communicative fluency, it reduces the main teacher's overwhelming contact hour burden, and they should be far enough ahead of the new students to be teaching them something. 3rd years could run a similar thing for 2nd years. 3rd year students should be able to run their own conversation times.
The final 2 non-contact hours should involve working on assignments, some home composition assignments, and maybe even listening to audio. It isn't so necessary to schedule this time.
With such a course I think you'd move fairly quickly. You should be into reading unadapted but simple original materials in the second semester. By the third semester I'd also set Donatus or Dionysius Thrax as reading, alongside a modern grammar, and be teaching some critical grammatical analysis (since most programs will not want to abandon this). The gains of an acquisition-orientation should pay off in the second half of a 3-year program, with the ability to set much longer texts/portions of texts for study, as well as requiring in language analysis and discussion.
In a seminary I'd readjust the system slightly. I'd assign more Koine reading than in a secular university, and integrate it into the NT courses. In 2nd and 3rd year the Greek reading should be integrated with doctrine as well, and in the right setting that would include Latin (come on you slackers!). Hebrew could undergo the same treatment. Of course, the seminary program is generally overloaded anyway. The student who turns up with some knowledge of Greek and/or Hebrew is off to a flying start.
Probably I've said all this before. Never hurts me to repeat myself (especially on the internet)