If she is separated from service from her place of employment that adminsiters the 401(k) in the year she turned 55, then indeed the withdrawal is penalty-free. The issue here is that since she continued in her job after the merger she was not "separated from service." The IRS defines separation of service as meaning "death, retirement, resignation, or discharge, and not when an employee continues on the same job for a different employer as a result of the liquidation, merger, consolidation etc. of the former employer" (details are here:
http://www.irs.gov/pub/irs-drop/rr-00-27.pdf ). Consequently the withdrawal incurs a penalty if she was under 59-1/2 years of age.
However, it would still be worthwhile to call the plan administrator to get clarification on this. If she wants to object to the code "1" on the 1099-R, she can file form 5329 with her tax return and indicate reason code 1 - which (to be confusing) on this form means she was separated from service at age 55 or later.