Can I ask why you think this is not the best way to achieve this? It looks like a good solution to me, if it is genuinely necessary to destroy the file contents irretrievably.
The advantage of this way of doing it are:
- the program already exists (so it's faster to develop); and
- the program is already trusted.
The second is an important point. It's possible to overstate the necessity of elaborately scrubbing files (Peter Gutmann, in a remark quoted on the relevant wikipedia page, has described some uses of his method as ‘voodoo’), but that doesn't matter: in any security context, using a pre-existing tool is almost always more defensible than using something home-made.
About the only criticism I'd make of your current approach, using system(3), is that since it looks up the shred program in the PATH, it would be possible in principle for someone to play games with that and get up to mischief. But that's easily dealt with: use fork(2) and execve(2) to invoke a specific binary using its full path.
That said, if this is just a low-impact bit of tidying up, then it might be still more straightforward to simply mmap the file and quickly write zeros into it.