Possible internal contamination from soaking or scalding slaughtered chicken in hot water to ease plucking I understand that a slaughtered chicken may become externally contaminated due to the impurities present in water. 


  Over the course of a processing day and despite scald tank
  temperatures of 50-60C, the water in scald tanks can become
  contaminated with salmonellas and campylobacters as a consequence of
  involuntary defaecation (Humphrey and Lanning, 1987; Mulder et al.,
  1978).  The bacterial load of the tank water can also be increased by
  microorganisms present on the feathers and skin of the birds (Mulder
  et al., 1978; Berndtson et al., 1992; Kotula et al., 1995; Q22-Q28
  Q23-Q29)  Kotula and colleagues (1995) report more than seven logs
  CFU/ml of rinse for both campylobacters and salmonella on some
  carcasses immediately before scalding.  When a carcass enters the
  scald tank, it is not unusual for water to be inhaled into the lungs
  (Thomson and Kotula, 1959).   If there is contamination present in the
  scald tank water and blood is still circulating in the carcass,
  bacteria can be transported by the circulatory system into internal
  organs and muscles.


Source: http://www.ukmeat.org/FSAMeat/PoultryScalding.htm

I am not talking about contaminations like the above. I am asking about any possible internal contamination. 

During scalding, do you think that the water is hot enough,
or the process is long enough, to substantially increase a whole chicken's core temperature, and  to actually start some internal body process (metabolism perhaps)? Since evisceration is yet to be done, are there any chances of the organ walls breaking down and leeching filth into the meat?  Is it possible for the filth to escape the organs and permeate the meat? We are assuming the organs themselves are neither punctured nor torn.

I may be talking about a very remote possibility, but I really need to know this.
Are you looking to do this for industrial purposes? Or are you just doing this at home? Also, what is your major concern - putrid water getting into the lungs and growing from there? The water should be hot enough to kill most bacteria at boiling after a relatively short exposure (anything from defecation or exposed on the feathers).

As for internal temperature, at a small home scale, I don't think it's that big of a deal. Whenever we slaughtered our chickens we always scalded them to remove the feathers, and never had any issue. Same with the hogs (removing hair).

Anything which may get kicked off internally should be halted/paused relatively quickly by proper sanitation and food prep techniques after plucking. If you are cooking the bird right away, you shouldn't have any issue because it would take awhile at room temperature for most bacteria to really start working their mojo. Assuming you slaughter, scald, defeather, clean, and then do whatever butchering is necessary (if any), you're talking about an hour to an hour and a half (generously). Afterwards, it'll go in a freezer or a refrigerator (both of which will slow the metabolism of any bacteria), or a pan (which will kill the bacteria using proper cooking techniques). There simply shouldn't be enough time IMHO. Now, I wouldn't let the bird sit around for a few hours, but that's pretty common sense.