CreateProcessでよいのでは?
他にも
exec系
fork系
ありそうですけど、試す気にはなりません
>でも、batファイルを作成するのはなしです。
#この書き方は微妙に回答減ると思いますよ。

popenは使ったことがないのでパスして
CreatePipeとCreateProcessで試してみました

CString Execute(CString strIn)
{
SECURITY_ATTRIBUTES saAttr ;
HANDLE hSaveStdOut ;
HANDLE hSaveStdIn ;
HANDLE hSaveStdError ;
HANDLE hChildStdoutRead;
HANDLE hChildStdoutWrite;
CString strOut ;

strOut = _T(") ;

saAttr.nLength = sizeof(SECURITY_ATTRIBUTES) ;
saAttr.bInheritHandle = true ;
saAttr.lpSecurityDescriptor = NULL ;

hSaveStdOut = GetStdHandle(STD_OUTPUT_HANDLE) ;
hSaveStdIn = GetStdHandle(STD_INPUT_HANDLE) ;
hSaveStdError = GetStdHandle(STD_ERROR_HANDLE) ;

if(!CreatePipe(&hChildStdoutRead, &hChildStdoutWrite,
&saAttr, 4096)) {
return strOut;
}

if(!SetStdHandle(STD_OUTPUT_HANDLE, hChildStdoutWrite)) {
return strOut;
}

PROCESS_INFORMATION Process ;
STARTUPINFO StartInfo ;
memset(&StartInfo, 0, sizeof(STARTUPINFO)) ;
StartInfo.cb = sizeof(STARTUPINFO);
StartInfo.dwFlags = STARTF_USESTDHANDLES|STARTF_USESHOWWINDOW;
StartInfo.wShowWindow = SW_HIDE ;
StartInfo.hStdInput = hSaveStdIn ;
StartInfo.hStdOutput = hChildStdoutWrite ;
StartInfo.hStdError = hSaveStdError ;

if(!CreateProcess(NULL, strIn.GetBuffer(), NULL, &saAttr,
true, CREATE_NEW_CONSOLE, NULL, NULL,
&StartInfo, &Process)) {
return strOut;
}

if(!SetStdHandle(STD_OUTPUT_HANDLE, hSaveStdOut)) {
CloseHandle(hChildStdoutWrite) ;
return strOut;
}
CloseHandle(hChildStdoutWrite) ;

DWORD dwOutRead;
DWORD dwRtn ;
bool bEnd = false ;
CHAR szBuffer[1024] ;
TCHAR* pDst ;
int sizeInput ;

sizeInput = 0 ;
while (1)
{
if(!ReadFile(hChildStdoutRead, szBuffer, 1000,
&dwOutRead, NULL)) {
dwOutRead = 0 ;
}
if(dwOutRead==0 && bEnd == true) {
break ;
}
if(dwOutRead>0) {
szBuffer[dwOutRead] = 0 ;
pDst = ConvertToUnicode(szBuffer) ;
strOut += pDst ;
delete [] pDst ;
}
dwRtn = WaitForSingleObject(Process.hProcess, 0) ;
if(dwRtn == WAIT_ABANDONED || dwRtn ==WAIT_OBJECT_0) {
bEnd = true ;
}
Sleep(10) ;
}

return strOut ;
}