Just repeating what I wrote in the other Kapporus thread:
Just glancing through the Mishnah Brurah, the use of a chicken, was a minhag that was favored by the Arizal. It is a symbolic gesture done to the chicken to help us understand what is stake this time of the year (and chas v'shalom something that we may deserve). The mishnah brurah also goes on to explain that in cases where there is a question where people will push to get the mitzvah done or that due to the mass shechitah that is taking place the shochet will not properly check his knife then money could be used instead. (So it suggested that the shochet should come to the house to avoid these problems something that I doubt to many of out wives would allow...lol)
There was also a suggestion of using money so that the poor person on the receiving end should not feel inferior or bad for getting the "sinner" chicken. So in these cases the value of the chicken should be given to the poor) However, if it is known that he/she would not care, giving the chicken is better so that there is less work for the poor person.
On an interesting side note, it also mentions that after the shechitah is done the entrails should be thrown on the roof (or similar place, of which we could not do today anyway due to saftey and health concerns) as a form of compassion to Hashem's creatures/ birds who will eat the remains which is a good thing to do before the onset of Yom Kippur.
However, this doesn't make all the kapporus centers get off the hook. (We have to separate the minhag which is a good thing according to the Arizal and many Achronim and the way that we set up the practice) Once they are organized the agency/party involved must take responsibility and accountability that the chickens are treated fairly and that the neighbors are not affected by the smell, noise, and remains of the chickens. If a person feels that there is a Tzar Ba'ali Chaim issue then don't use them and advocate for a better system. In our neighborhoods the chickens are brought in shifts. Once used for Kapporus, they are taken back to the farm or place where they will shect them and the time in the crates are kept to a very minimum.