+ 1 to what "jvblack" wrote on how to turn the speaker off within the software.  That is exactly correct. 

Or you can disconnect the speakers inside the open back cabinet and leave them unplugged as long as you use a closed back cabinet of ANY KIND that matches the minimum Ohm load per channel.

My personal favorite answer to this question it to ask a question first.  How loud do you play on stage?  You've written that you've turned the low Q down and you still get "uncontrollable low frequencies especially when palm muting".

I've had a Vetta 2x12 combo since 2003 with the original Celestion Custom 90 speakers in it and have never had this problem.  I play a variety of material and I can't even play my amp with FULL POWER MODE on.  I use HALF POWER mode and I get more than enough volume for any style of music I play heavy metal or not.  I also do not play a 7 or now 8 string guitar, but I DO have custom tunings I've created on my Variax guitars that are tuned down to "B" like a Baritone guitar is tuned with no bass "overload" problems.  If you're like most metal players I've worked with live or in the studio - they have this weird EQ thig they do where they THINK they are getting the sound they hear by their favorite metal players, but in reality they are far from how that sound is accomplished.  These guys I've worked with scoop out nearly all the mids and crank the highs & lows.  That is precisely the opposite way of getting that mean crunk for playing metal.  But I digress...

Please don't try making your combo into a head, do as previously suggested if the knobs are not where you want them...buy a used good condition Vetta II head and perhaps sell your Vetta combo.

ALso, I've found that using my Line 6 Vetta and opther Line 6 gear that produces acoustic guitar sounds (don't know if you ever need this or not) The BEST cabinet solution is a good (4ohm for mono or a pair or 8ohm for keeping the stereo output the same) BASS CABINET by several of the better bass cabinet makers.  I don't recommend PA cabs for this as nearly all of those horns are NOT adjustable as they are on bass cabs with horns or tweeters.

Oh, and you always do have the option of using a stereo power amp (tube or solid state) from your Vetta into any cabinets you choose.  This would give you the option of using your internal speakers, PLUS using the external amp and speakers.  One with a VARIABLE horn and my personal preference is one with 10" speakers. 

BUT if you want more bottom end, go with one with 12" or even a combination of 10/12 with a 15".  These cabs are ALWAYS closed backed for the PUNCH gained by the air compression within the cabinet that MOST guitar cabs don't have, PLUS you gain the added bonus of having a full range cabinet that can produce shimmering high Q if needed for acoustic patches.

And it that is still not enough frequency control for you - you also can add a stereo 31-band Graphic EQ cheaply from Behringer or other company that makes quality gear at inexpensive prices.  In this manner you not only do not have to make severe EQ setting within the patchm, but just let the amp "cruise" at a nominal volume and crank up the external amp/EQ and that will come out of whatever external cabinets you have connected to the external power amp.

I hope this helps you in your decision making.  Perhaps other might even get some ideas based on my out-of-the-box thinking in matters like these?

Take care,

Neal