1. Latin is a dead language. It's pointless to worry about details of pronunciation. Scholars argue about how Shakespeare spoke, and even Jane Austen, and they only died a few hundred years ago. I doubt any Roman of Caesar's time would recognise any kind of Latin speech as taught today.
2. Scientific names are Latinish, not Latin, anyway. They're Latinized Greek (Latin endings grafted onto Greek stems) or English (Latinized proper -- Linnaeus-- or place -- montevidensis-- names) or whatever. Often misspelled, too.
3. Biologists' pronunciation is neither Latin we learned in school (where we said "Kikero" nor church Latin (where we'd sing Sisero under most conductors) nor any other system. For one thing, Latin vowels are very pure (no dipthongy elisions such as we Americans tend to inflict on any and all vowels) and absolutely consistent -- they don't change according to what consonant they're next to. Properly spoken, Latin is also very unaccented to most ears -- we're used to heavy accents on one or another syllable, and also uneven duration. None of these is particularly observed in biological circles and I've been to conferences where three different PhD ecologists or botanists (plants are my thing more than birds) pronounced an uncomplicated name three different ways.
4. I see no need for anyone to be embarrassed about pronouncing Latinish names under any circumstances. If some person attached to his (or more likely his latest mentor's) particular idea of pronunciation should smirk, you can smirk right back and say "Oh, I'm sorry, I'm so used to Church (/Medieval) Latin pronunciation, how did you pronounce that?" (Do not try this if your professor is also a priest.) Or "Oh, I'm sorry, Classical Latin is so different from these macaronic forms." Or whatever comes to mind.
As for your research, that's simple. Eavesdrop on the professor and if necessary take notes and do it exactly his way. You can have lots of fun setting him up to say the names of your research subjects. (It's a pretty good working hypothesis that if your professor/research director/whatever is picking at you or anyone else about pronunciation what he means is "say it my way.")
Don't get me wrong -- never mind that this is one of my pet peeves, Latin is the most useful language I ever took in school (I'd be ashamed to say I "learned" it). For one thing, it's everywhere, in common as well as technical speech. I expect you can get a working knowledge of the meanings of the common stems about as well paying some mind to the translations of scientific names as anywhere, these days.