Pitaya Red Velvet Cake became brown Starting point:

I was trying to follow a red velvet cake recipe from the internet, but since I always try to replace industrial/artificial ingredients by more "natural" ones (just out of curiosity), I decided to replace the buttermilk and the liquid red food color with red pitaya pulp (which is tasteless and mostly made of water, similar to carrots, which can also turn into good cakes). 

The recipe I've found is as follow:

! – 200ml of (whole) milk
  – 1 table spoon of lime juice
  (left to rest for 10 minutes) 
             -&gt; replacement for buttermilk (which is unusual to find here)
  //
  – 3 teacups of wheat flour
  – 2 teacups of sugar
! – 1 table spoons of cocoa powder
  – 3 tea spoons of baking soda (1 table spoon)
  – 1 tea spoon of salt
! – 1 table spoon of baking powder
  //
  – 100g of unsalted soft (non-refrigerated) butter
  – 2 eggs
! – 3 tea spoons of white vinegar (1 table spoon)
  – 1 tea spoon of vanilla extract
! – 4 table spoons of liquid red food color
  – 5 more table spoons of lime juice

and I've changed it to that:

! – 300g of fresh red pitaya pulp
  – 1 table spoon of lime juice
  //
  – 3 teacups of wheat flour
  – 2 teacups of sugar
! – 1 table spoons of cocoa powder
! – 5 tea spoons of baking soda
  – 1 tea spoon of salt
  //
  – 100g of unsalted soft (non-refrigerated) butter
  – 2 eggs
! – 4 tea spoons of white vinegar
  – 2 tea spoons of vanilla extract
! – 2 table spoons of anatto*
  – 5 more table spoons of lime juice

Besides replacing milk and food color with pitaya pulp (turned to juice), I added 2 table spoons of anatto and replaced the 1 table spoon of baking powder with 2 more tea spoons of baking soda and 1 more tea spoon of vinegar, since I always do this for every cake recipe.

Result:

Perfect in matters of structure/texture, taste and smell... BUT after half of the time in the oven, it started turning from a dark reddish purple to honey cake brown.

 -> 

Question:

Was my idea of replacement a guaranteed failure with regard to the resulting color? did I missed something? Is there any trick or technique I could/should try to preserve the natural color of pitaya through the baking process? More acid ingredients, like lime juice? Less of them, maybe? Does anyone knows how much heat can pitaya pigments (betalain?) take before stopping giving vivid colors (?) and if there are any other natural red/purple pigment more heat-resistant (?). (note that its vivid color survived until half of the baking process)
Note that carrot cake isn't the bright orange of raw or even boiled carrots either.  This is especially true of the crust and from your description of partway through cooking I suspect that's the colour you're looking at.  If the inside is much better, there's still hope.

Many colourful compounds in plants aren't stable under heat, but even ignoring that, sugar and flour both brown on the outside of cakes. Both caramelisation and the Maillard reaction (the former is probably more important in cake) take place at typical oven temperatures, so you may have some success with a cooler oven.  This is a moist recipe so it may not turn out too dry, but you may want to cover it for the end of the cooking time.  A cheating approach is to cut the crusts off, then ice all over.

I've had a play with DIY plant extract colouring and the crust colour is clear (I didn't make enough extract, and was going for orange) You may want to look at anthocyanins, in fact given your comments about acid you may already have done so