| Yevamot
"And if the man does not want to take his brother's wife, then his brother's wife shall go up to the gate unto the elders, and say: 'My husband's brother refuses to raise up unto his brother a name in Israel; he will not perform the duty of a husband's brother unto me'... then shall his brother's wife draw near unto him in the presence of the elders, and loose his shoe from off his foot, and spit in his face; and she shall answer and say: 'So shall it be done unto the man that doth not build up his brother's house'" (Devarim 25:7,9). The biblical text is quite clear that yibum is the preferred option.
Yet, as is often the case, the oral tradition presents a more nuanced and complex picture[1]. "The mitzvah of yibum takes precedence over the mitzvah of chalitzah--initially, when they intended for the mitzvah; now that they do not intend for the mitzvah, they said that the mitzvah of chalitzah takes precedence over the mitzvah of yibum" (Yevamot 39b). The Torah allows what would otherwise be considered a form of incest in order that one may "build up his brother's house". But marriage to one's sister-in- law for any other reason--such as love--would apparently nullify the mitzvah.
Just how important proper intent is can be seen in words of Abba Shaul: "If one marries his sister-in-law on account of her beauty, or in order to gratify his sexual desires or with any other ulterior motive, it is as if he has infringed the law of incest; and it is close in my eyes that the child [of such a union] is a mamzer, illegitimate child". As understandable as Abba Shaul's position may be, the Sages disagree. "But the Sages said: 'Her husband's brother shall cohabit with her', whatever the motive".
Proper motivation in mitzvoth is ideal, but that is all it is--an ideal, not something that would prevent us from doing a mitzvah, in this case yibum. Regardless of one's motivation, a mitzvah is a mitzvah[2]. "Rami bar Chama said in the name of Rav Yitzchak, 'It was re-enacted that the precept of the yibum is preferable to that of chalitzah'" (Yevamot 39b). To the Gemara's question, "Did the moral level of people improve?" he answers no, but while he initially followed the view of Abba Shaul, he now feels we should follow the view of the Sages, downplaying the importance of motivation.
The role of motivation is captured with the well-known teaching of our Sages: "One should always be involved in Torah and mitzvoth without being properly motivated as, from lack of motivation, one will eventually become properly motivated" (Pesachim 50b). How or even whether this idea can be applied to yibum would seem to be the basis of the debate between Abba Shaul and the Sages.
The Netziv, writing in 19th century Lithuania, explains (Meisheev Davar 1:46) that such leeway in performing mitzvoth with impure motivations only exists if one is actually obligated in a mitzvah. One cannot exempt oneself from an obligation because one is not properly motivated. We must do what we must do. However, when it comes to a mitzvah which is not an actual obligation--starting a new shul when a neighborhood shul already exists is the example he uses--the Netziv claims motivation is key. When one volunteers to do a mitzvah, one must volunteer for the right reason. It is for this reason that we daven every Shabbat that G-d should bless "those engaged in communal work b'emunah, in faith". There is no greater mitzvah than communal work, but such should be done only by those who put the needs of the community first[3].
Perhaps Abba Shaul argues that with an option of chalitzah and the great difficulty of proper motivation of yibum, chalitzah should be the default option. The Sages, on the other hand, view yibum as the ideal, with chalitzah a poor second choice--why else spit on one who chooses this option? Yibum in this respect is no different from many other mitzvoth, where our motivation may be weak but the importance of the mitzvah itself obliges us to perform it no matter our motivation.
[1] Why this is so is beyond the scope of this forum--and requires the elucidation of experts greater than I. One approach to ponder is that the Written Law is written from a Divine perspective with its focus on strict justice and perfection, whereas the Oral Law reflects the Torah as it must be applied in the real non-perfect world, where justice must give way to mercy, truth to compromise. Thus, to cite one of many, many examples, the death penalty abounds in the Torah as truly befits one who violates the will of G-d. Yet no lesser a Sage than Rabbi Akiva declared that had he been on the Sanhedrin (it having been disbanded 40 years before the destruction of the Temple), no one would have ever received the death penalty (Makkot 7a). Theory and practice often differ.
[2] Motivation, lishma, is not to be confused with intent, kavanah. The former deals with why I am doing the mitzvah, while the latter ensures that one is cognizant that he is performing a mitzvah. Whether one requires intent, and the exact intent required, is a complex topic discussed in various places in the Talmud. Motivation presupposes intent--one cannot speak of intent if there is no awareness of the mitzvah in the first place.
[3] One who is motivated by personal gain yet involves himself in communal work is liable to do much more harm than good, making motivation that much more important than when dealing with personal mitzvoth.