As a shameless personal plug, I've actually written a node about how you can fool a process into thinking that it is connected to a terminal when it is not. This may not be of the utmost use to you in fixing your problem... but it is apropos.
That is not needed here.
The OP says that the command runs fine in backticks, but hungs when runs with system. The program probably waits for input (confirmation) when run on a terminal, that's why it hangs. What the OP actually needs is to fool the program it's not running interactively, by calling it through a backtick or redirecting its stdout. This is much simpler to acheive. It might even be unneccessary if the program has some command line switch to force it not to ask questions. Many programs like rm or fsck have such an option: if you give rm a file for which you do not have write access, it promts you whether you want to delete it, you can override this with the -f switch or by redirecting its stdin. Running rm in backticks redirects the stdout which is not enough for rm: it prompts for a confirmation, even if stderr is redirected too, and if you don't see the error it appears to hang.