With the advent of SHAttered, does Oracle have any plan to support
later SHA versions for SecretKeyFactory?
First, they don't need to. We are talking about PBKDF with HMAC-SHA1 here, which is a password-based key derivation function.You don't need collision resistance (which is the only property SHAttered broke) for password hashing, in fact it is trivial to find two passwords that hash to the same value with PBKDF2. What you really want from a password hash is one-way-ness / pre-image resistance (ie you can't recover the input from the output) other than using generic attacks.
Second, as of JRE8 you can use any pseudo-random function (PRF) the API knows instead of HMAC-SHA1 already and in fact HMAC-SHA256 is given as an example in the documentation.
What are the alternatives?
You don't use PBKDF2 from the standard library but rather use a binding to a more advanced password-based key derivation function such as Argon2, which has at least bindings for Java.