Your translation sounds very good already (I'm a native speaker). If I force myself to come up with a variation of it, I got:
「原」という漢字は知っていましたが、「わら」と読むとは知りませんでした。
The most significant difference here is the use of 「~しました」 for the first 「知る」; since you use 「~でした」 for the second 「知る」, it sounds more natural to use 「~します・しました」 form there. (Use of the past tense is just a matter of taste.)
UPDATE
Since I can't comment yet, I'm answering to the comments here;
@user4092 Yes, that's more correct; I missed it. Omitting 「は」 from 「だとは」 makes you sound more casual. But 「は」 here also gives another implication. See below.
@Flaw In that case, I usually say something like 「この/その漢字を『わら』と読むとは知りませんでした」.
Combining the two points, you can say:
「この/その/『原』という漢字を『わら』と読むとは知りませんでした」
Here, 「知っていましたが」 is now omitted. 「とは」 in 「読むとは知りませんでした」 implies that you know something about the kanji other than how to read it. In this case, how to write it or that you have seen it.