"She's applying to a lot of schools: MI Tech, UM, Duke, Stanford, Case Western, Valparaiso, Vanderbilt, Calvin, Rose-Hulman, Colorado School of Mines, LeTourneau, Geneva, Cedarville (don't have civil so she'd have to major in mechanical instead), Messiah, Stevens, and UIUC. Also looking into maybe applying to Rice and Northwestern. I know the list is long... we are just hoping that a few of them will offer her some decent merit scholarships."
Rose-Hulman is definitely a small school that puts an emphasis on hands-on projects while also teaching the necessary theory. RH also offers signficant merit aid. My son really liked the school but in the end decided against it because of its location. The Michigan schools are obviously well known for their quality engineering education but are also very very large institutions. I'll plug Va Tech (very large but not as large as UM) that is known for "hands on - minds on" approach to education. They have a lot of cool labs; students are required to work on projects; and they have a living learning community for female engineers. I think your daughter would get some merit aid but not sure how much.
Most large state universities will have co-op internships and study abroad. So, look for any differences that might be of special interest to your daughter. For example, do they have special mentoring opportunities for female engineers?
Some of the schools on your list (e.g., Duke, Stanford) are prestigious but quite expensive even with likely aid and may not offer any advantage in civil engineering. Since your daughter hasn't started yet it may be wise to go with a university that offers a complete range of engineering majors.