That's exactly the problem. Google, as a software company, doesn't currently have to worry about a lot of the issues that the hardware side of Motorola does, like supply chain management(both on the production and disposal side), dealing with retail outlets, directly dealing with cellular service providers as a device manufacturer, governmental agency compliance for hardware, etc. Google doesn't have really any experience with this, which means they absolutely need to keep the people that are currently doing those jobs.
Also, from what I've heard from people that used to work there, Motorola's engineering culture is on the "very corporate" side of things. Integrating that into Google's rather loose culture will be difficult, I think. This is especially important because both sides will need to be working with each other very closely.
Best case, Google doesn't change much, and integrates Motorola's hardware chain well. However, if they do exert a lot of control over the hardware side, quality could decline in the short term as the issues I mentioned above get worked out.
Overall, I think it's a much stronger position for both companies. Motorola gets Google's software expertise, and Google gets Motorola's hardware engineering and supply chain.