This may not help you with the binary .doc format, but for the newer .docx format, I was able to get to the equation, which is embedded as an OLE document, using the following code:
InputStream in = new FileInputStream(f);
XWPFDocument doc = new XWPFDocument(in);
for (PackagePart p : doc.getAllEmbedds()) {
POIFSFileSystem poifs = new POIFSFileSystem(p.getInputStream());
byte[] oleData = IOUtils.toByteArray(
poifs.createDocumentInputStream("Equation Native"));
}
And then you can extract the MathType data in there and hand it to a MTEF parser.
If you don't need the MathType data, there is also a placeholder image (in WMF format) that just renders the equation.