Using a cover version of the song is better, for a mainstream commercial like this, because it emphasizes the purity of the songwriting. Morrissey and Marr would be even more appreciated than they already are if their songs were occasionally wrenched out of the context of The Smiths (i.e. they're miserablists, faded 80s icons, militant vegetarians, embroiled in court battles, etc.) and evaluated on their own merits. As a cover version, the sentiments in "Please Please Please" sound universal, not like another example of Morrissey's moodiness. Writing for "everybody" was always his intent.
And let's not forget they started off with a plan to write songs solely for other artists to record, an idea that fortunately had the lifespan of a fruit fly. The ad makes sense. It underlines the fact that The Smiths are practically an institution in the UK. I just hope they wait 10 years before allowing the next ad to go out.