- Is this (cryptographically) secure?
That is hard to say without knowing the exact details of the bitcoin protocol (which I would like to understand better, but don't have the time at the moment). Looking at the document you linked to, the public child key is created as $\text{HMAC-SHA512}(Key = c_{par}, Data = ser_P(K_{par}) || ser_{32}(i))$. This value is split in half. One half is turned into a point. That point, plus $K_{par}$ is returned as the public key. The other half is returned as the chain node. Is this the index of which you speak?
The process looks good, but it is hard to say whether or not it is cryptographically secure without knowing details of how the input parameters are chosen. It all comes down to the entropy of those. If they are high entropy, then the output should be high entropy and so it should be "secure" (you haven't actually defined secure, but I'm assuming you mean that an outsider could not guess/figure out the key).
I would strongly recommend, once you have formally specified your protocol, that you work on a security proof. This will likely be done by reducing the security of your protocol to some other (related) protocol. This would be done by assuming an attacker breaks your protocol then showing some horrible impact this would have on the other protocol. The other protocol could be the HD wallet protocols. That would establish that breaking your protocol is at least as hard as breaking HD wallet.
- Would it be better to hash the public keys before using them as an encryption key?
As the public key is a point on an elliptic curve, I would say yes. In particular, owlstead's recommendation of a key derivation function is on the right track.
- Are there any resources about doing something similar I can use for research?
Not that I am aware of.
- Anything blindingly obvious that I'm missing?
Well, if there is, I am missing it too. The best way to find out about this at this point would be to write up a short white paper on the idea and present it to people familiar with the areas (both bitcoin and cryptography). You could do this by sending it directly to researchers and getting their thoughts, publishing it in a workshop of some sort, etc. Also, make it available online somewhere (e.g., ePrint) and comment on here with a link (I'll definitely take a look). Your white paper should review enough of the basics of the bitcoin protocol and the HD wallet protocol so as to be self-sufficient. This should be a good exercise as I saw on your profile that you are a graduate student.