Como hacer que windows defender permita un .exe?

Si el exe no es dañino.

Si pasas el binario a hexadecimal ya lo puedes escribir en texto plano y puedes meterlo dentro de un script.

mira el siguiente código batch (vbs) en el que se integra cursospos.exe, el script lo escribe en binario lo ejecuta y luego lo borra y nada impide nada.
Código
@echo off
setlocal enabledelayedexpansion
 
Rem cursorpos and colorshow created by Antonio Perez Ayala
Rem http://www.dostips.com/forum/viewtopic.php?f=3&t=3428
call :heredoc cursorpos >cursorpos.hex && goto endCursorpos
4D5A900003[3]04[3]FFFF[2]B8[7]40[35]B0[3]0E1FBA0E00B409CD21B8014CCD21546869732070726F6772616D2063616E6E6F74
2062652072756E20696E20444F53206D6F64652E0D0D0A24[7]55B5B8FD11D4D6AE11D4D6AE11D4D6AE9FCBC5AE18D4D6AEED
F4C4AE13D4D6AE5269636811D4D6AE[8]5045[2]4C010200EB84E24F[8]E0000F010B01050C0002[3]02[7]10[3]10[3]20[4]40[2]10
[3]02[2]04[7]04[8]30[3]02[6]03[5]10[2]10[4]10[2]10[6]10[11]1C20[2]28[84]20[2]1C[27]2E74657874[3]4201[3]10[3]02[3]02[14]20[2]60
2E7264617461[2]F6[4]20[3]02[3]04[14]40[2]40[8]E806[3]50E81301[2]558BEC83C4E06AF5E81201[2]8945FC8D45E650FF75FCE8
FD[3]668B45EC668945E4E8BC[3]E8DB[3]803E0075058B45EAEB5C803E3D750646E8C6[3]668B4DEAE84A[3]8945EAE8B5[3]803E
007418803E2C750646E8A5[3]668B4DE4E829[3]668945EC8B5DEA53FF75FCE8AE[3]8D45E650536A018D45E350FF75FCE895[3]0F
B645E3C9C333C032DB33D28A164680FA2B740880FA2D750980CB0280CB018A164680FA30720F80FA39770A80EA306BC00A03
C2EBE9F6C301740BF6C302740366F7D86603C14EC3CCCCCCCCCCCCCCCCCCCCCCCCCCE847[3]8BF08A06463C2275098A06463C
2275F9EB0C8A06463C20740484C075F54EC38A06463C2074F94EC3CCFF2514204000FF2500204000FF2504204000FF250820
4000FF250C204000FF25102040[191]6E20[2]8C20[2]9C20[2]BA20[2]D620[2]6020[6]4420[10]E820[3]20[22]6E20[2]8C20[2]9C20[2]BA
20[2]D620[2]6020[6]9B004578697450726F6365737300F500476574436F6E736F6C6553637265656E427566666572496E666F
[2]6A0147657453746448616E646C65[2]380252656164436F6E736F6C654F757470757443686172616374657241006D025365
74436F6E736F6C65437572736F72506F736974696F6E[2]E600476574436F6D6D616E644C696E6541006B65726E656C33322E
646C6C[268]
:endCursorpos
 
call :heredoc hexchar >hexchar.vbs && goto endHexchar
Rem Hex digits to Ascii Characters conversion
Rem Antonio Perez Ayala - Apr/14/2012
 
Dim line,index,count
line = WScript.StdIn.ReadLine()
While line <> ""
   index = 1
   While index < len(line)
      If Mid(line,index,1) = "[" Then
         index = index+1
         count = 0
         While Mid(line,index+count,1) <> "]"
            count = count+1
         WEnd
         For i=1 To Int(Mid(line,index,count))
            WScript.StdOut.Write Chr(0)
         Next
         index = index+count+1
      Else
         WScript.StdOut.Write Chr(CByte("&H"&Mid(line,index,2)))
         index = index+2
      End If
   WEnd
   line = WScript.StdIn.ReadLine()
WEnd
:endHexchar
 
:: Crear cursorpos.exe
cscript /nologo /B /E:VBS HexChar.vbs < "cursorpos.hex" > "cursorpos.exe"
del cursorpos.hex
del hexchar.vbs
 
cls
cursorpos
cursorpos=4,5
echo hola mundo
echo.
del cursorpos.exe
goto :EOF
 
:heredoc <uniqueIDX>
setlocal enabledelayedexpansion
set go=
for /f "delims=" %%A in ('findstr /n "^" "%~f0"') do (
    set "line=%%A" && set "line=!line:*:=!"
    if defined go (if #!line:~1!==#!go::=! (goto :EOF) else echo(!line!)
    if "!line:~0,13!"=="call :heredoc" (
        for /f "tokens=3 delims=>^ " %%i in ("!line!") do (
            if #%%i==#%1 (
                for /f "tokens=2 delims=&" %%I in ("!line!") do (
                    for /f "tokens=2" %%x in ("%%I") do set "go=%%x"
                )
            )
        )
    )
)
goto :EOF