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A Japanese teacher on Twitter posted that 化学 is pronounced かがく and means "chemistry". I double-checked it on tangorin.com and it lists that pronunciation but says that it's pronounced ばけがく to avoid confusion with 科学 ("science").

I can't find any more info on the net about this... could somebody confirm this?

In particular, for my Anki vocabulary deck, which pronunciation should I learn? Or should I shoehorn both into my deck somehow?

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I think the basic word is かがく, but the other reading is possible. Here's what 明鏡国語辞典 says at the bottom of its entry for 化学{かがく}:

►「科学」と区別して「ばけがく」ともいう。

If you pronounce it this way, you're deliberately using the other reading of the first kanji to make sure the person you're talking to knows which word you mean. I would definitely learn the reading かがく, though.

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Other examples of intentionally altered readings to avoid confusion:

  • 私立【しりつ】 (private) & 市立【しりつ】 (city-run) →　私立【わたくしりつ】 & 市立【いちりつ】
  • 売春【ばいしゅん】 (selling sex) & 買春【ばいしゅん】 (buying sex) → 買春【かいしゅん】
  • 波線【はせん】 (wavy line) & 破線【はせん】 (dashed line) → 波線【なみせん】 & 破線【やぶれせん】
  • 市長【しちょう】 (city mayor) & 首長【しゅちょう】 (mayor in general) → 首長【くびちょう】

Learning only ばけがく is not recommended. Personally, I'd rather use orthodox readings (on the left) whenever I can, because the altered ones (on the right) sound more or less jargon to me.

Although avoiding ばけがく is not always possible, of course, I would sometimes use "ケミストリーの化学【かがく】" instead of ばけがく, when I'm sure the listener can understand; but this is no more than my personal preference.

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    I feel like the 売【ばい】・買【ばい】 issue must come up a lot. It always struck me as weird that these two antonyms have the same reading (and even show up in the same word - 売買).
    – senshin
    Commented Jun 18, 2014 at 15:29
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    @senshin That right there is an excellent justification for why Japanese needs kanji, thinking about it. Take those words written in kana and even with context it would be hard to tell which was intended.
    – Kaji
    Commented Jun 18, 2014 at 15:56
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    @senshin, re: Chinese, both 売 and 買 are simply two sides of the same activity, so it kinda makes sense that they're almost the same word: 売 (mài, high falling tone), 買 (mǎi, low tone rising slightly at the end). For that matter, Japanese 買う is, at its root, the same word as 代う, 換う, 替う, 交う, all かう with a root meaning of "to trade, to swap, to exchange". By extension, these are the roots of かわる・かえる "to change".
    – Eiríkr Útlendi
    Commented Jun 18, 2014 at 16:56
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    @EiríkrÚtlendi You can see the relationship in the older forms of the characters, too: 売 was formerly 賣, which is 士 over 買, and 士 here is a simplified form of 出, so 売(賣) = 出＋買 "put out for buying" = "sell".
    – user1478
    Commented Jun 18, 2014 at 17:04
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    To me, if anything, this topic illustrates why Japanese might not need kanji; without them alternative words such as ばけがく would spread spread more quickly and gain acceptance. After all, there seems to be a need for such alternatives even now with kanji.
    – blutorange
    Commented Jun 18, 2014 at 21:39

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