Some people argue that the use of "障害者" is politically incorrect, because the kanji "害" has the meaning like "to harm". Because of this, there has been shift to "障がい", especially in media and official documents. It seems 障がい was first seen in 1990s on newspapers. On the other hand, some people think that it is oversensitive, and that the mixture of kanji and hiragana is weird. Anyway there has been some arguments over this (try, for example, searching google for 障害+表記+site:go.jp).
Historically, (as you probably know), 障害 was written as 障碍 or 障礙． Here, "碍" (=礙), as used in 碍子, simply means obstruction, without the negative tones that 害 has. In accordance with the introduction of 常用漢字, which neither 碍 nor 礙 is listed on, those kanji-s were eventually replaced by 害. Because of this, some people (including me, by the way) think that using "障碍" or "障礙" will settle the problem. Newspapers will never use this for now because it isn't listed in the joyo-kanji list, and I don't know if there is any movement towards listing them. It was at least actually discussed in national diet (question and answer to that).
I don't know what ratio of the people think it is (politically incorrect vs not a problem) or (important vs irrelevant vs I don't care).