Rfc2898DeriveBytes implements the standard algorithm known as PBKDF2 and defined in RFC 2898 (hence the name). That algorithm uses a configurable underlying pseudorandom function, which is usually HMAC, and HMAC itself relies on a configurable underlying hash function, usually SHA-1. While all of this is configurable, a given implementation might not be as flexible, and, indeed,
Rfc2898DeriveBytes always uses HMAC and always uses SHA-1 as underlying function for SHA-1.
Nowadays, the people collectively known as "auditors" tend to wail, whine, scream, mock and run in circles when they see anything that involves SHA-1. This is scientifically unwarranted. Right now, among all the published Science, there is not the slightest indication that SHA-1 when used in HMAC would be weak. Known weaknesses in SHA-1 are about collisions which do not impact HMAC (and these are still theoretical anyway). If some guy with a CISSP insists that SHA-1 actually makes PBKDF2 more vulnerable to brute-force, then that guy should go relearn his lessons.
Nevertheless, switching the SHA-256 is not a bad idea, so if shunning SHA-1 is what it takes to get rid of auditors, so be it.
However, the following must still be said:
Disassembling then modifying is a rather crude method and tends to lead to unmaintainable code. You could simply start from the actual source code (e.g. from here), or, even more simply (and with a cleaner legal status), reimplement it from scratch. .NET provides a HMAC/SHA-256 implementation; using it to do a PBKDF2 code is not hard.
Alternatively, you may try to reuse some other existing implementation, like this one.
You use PBKDF2 when you want to "hash a password", and not all functions are equal in that respect. A hashing function is any good only insofar as it is expensive for attackers to compute. In that respect, PBKDF2 with SHA-1 or SHA-256 is not the best choice; arguably, PBKDF2 with SHA-512 is a better deal (because existing GPU have a harder time optimizing SHA-512 than SHA-256), but other solutions may be preferable, in particular bcrypt. For more on this subject, read this, and more generally this.
This means that while SHA-1 "weaknesses" do not make PBKDF2 weaker, it still is a function that can be very well optimized on GPU, which is, in that case, a problem -- but, and that's the important point here, SHA-256 fares no better.
In any case, by using a pure C# implementation, you accept that this specifically CPU-intensive will run with the inherent slowdown of that technology, which can be estimated to a factor of 2 to 3 when compared with optimized C code (or assembly). In other words, you give an advantage of 2x or 3x to attackers. Therefore, you might want to use some native code here, not pure C#.