I've run into this too... SMS uses system, not good enough for some as I call
it poorly written programs. To get around the problem, I created a domain
user with "read and execute" to SMS distribution shares and is also a local
admin on workstations then used "freeware" autoit (there are paid programs
out there that do a better job of encryption of the exe but autoit fits my
needs),
http://www.autoitscript.com/autoit3/ to create an encrypted exe with runas rights. Then I used SMS to push the
autoit exe I created to install the program. It took me awhile to figure out
how get it to install from current location (install from SMS distro share)
but install from a network share with runas is a piece of cake.