The Answer: Technically yes, but the film has always been this way in the US.

Some people have been upset after seeing MGM's new Wild At Heart dvd by what they perceive to be tampering by Lynch in the same vein as the digital blurring of Laura Harring on the DVD of Mulholland Drive. But in this case, Lynch is not really to blame, and the film has always appeared with this change here in the US. It's only in recent years that people have been easily able to compare the domestic and foreign versions due to the internet and region free PAL/NTSC capable dvd players. So it's understandable why some might think this is a new change. But it's not.
When Wild At Heart was initially submitted to the MPAA for its rating, they would not give it a R due to the scene of Bobby Peru's head being blown off. Remember, this was in the days before there was an NC-17 rating (which even today is often considered undesierable for financial reasons), and X was pretty much only the domain of porn films. In order to pass it, an explosion and smoke were added to the scene to obscure some of the gore (the only other option being to cut the shot altogether). The MPAA approved the change and the film was given an R rating in the US. Since this requirement didn't effect the release of the film in any other countries, the shot was left untouched in all other releases. But here in the US, that shot has always been altered, from the original theatrical release down to the current dvd (which is the US release version, seeing as it's a US dvd.

Here's some proof just to put aside any doubts that this is not a new change.
The following photos show the shot from the original US VHS release of Wild At Heart:

Now let's take a look at the original US laserdisc version:

And lastly, MGM's new DVD:

As you can see, all three US versions (color and brightness issues aside) are the same, as was the original theatrical version. It's always been this way here in America. Just chalk it up to one of those rare occurrences where the MPAA was concerned about violence instead of their usual puritanical views on sex. Of course, given how far the envelope has been pushed today by modern action films, the scene would probably pass unaltered with a R rating today.

Here's the uncut shot from the overseas versions, just to see what all the fuss was about:


See, nothing too major, especially as the shot lasts barely a second. What's funny is, they could have restored the unaltered shot, slapped an "Unrated Edition" logo on the top of the dvd cover and probably sold a few more copies. But for whatever reasons, the decision was made to stick with the R cut. Since this is the way it was first (and always) released here in the US, I see no problem with presenting the original US theatrical cut on a US dvd release, especially when the change is so minor.

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