Apply to Geoscience PhD with GIS Masters

[qocha_geog]

I am about to enter my undergraduate senior year as an Earth Science Major (Geology concentration) and wanted some input on one potential post-grad route I'm considering. In the long run I know I want to do research, but at the moment am lacking confidence in the strength of my application if I applied to MS & PhD programs this application cycle. I wouldn't say I'm a horrible candidate, but my research activities have been somewhat scattered (no long term attachment to one prof or lab, although that is changing going into senior year), and there are a few less than desirable facets of my transcript (a couple low grades in intro science courses).  While I think I'm on an upward trajectory I don't think I would be strong enough to get into the caliber of program I would wan't or think myself capable of.

So one option I have been mulling over is that my current university has a 1 year GIS Masters. Most of my research thus far has been remote sensing oriented, and I have good relations with many of the people connected to the program and have performed well in courses cross-listed with the masters program, so I would be fairly confident about being accepted to the program. My thinking is that this would be to have an extra year to  hone a complementary skill set to Earth Science, and keep the momentum I'm building going, and further develop my current research  (I would likely be able to continue my senior thesis research for the masters).  

I do however a few reservations, the masters is housed in my university's school of design, not the earth science department, and is largely geared for city planning, landscape architecture types. While I'd have a fair amount of flexibility to tailor the course of study, it would still not strictly be an science degree, although it does include advanced programming and statistics components.  Additionally it is a professional, not a research masters, there is a senior capstone, however it appears less rigorous than a masters thesis.

After this I would plan on applying to Geoscience (or potentially Geography at some places if thats where they house remote sensing people) PhD programs and wanted to know if anyone had insight on how admissions committees would view this. Even if I explain my reasoning, and go out of my way to 'make the program my own'  by coupling it with additional research. would people view it as an indication that I'm an unfocused dilettante? Would it be at best a neutral? Would the fact thats its not an MS degree immediately render it useless?

I was hoping the degree and additional research would add a interesting angle to my resume but could also see it working against me. I don't want to be in school forever, but would it be better to get the GIS degree then apply to MS Geosceince programs?

Also a few extra points that might matter: my current Undergrad institution is very prestigious (Ivy Leauge, top 10 over all), the earth science department however is quite small with a few standout profs but definitely not a destination dept. The Graduate Design School on the other hand is extremely well regarded and has the benefit of having one of the historical giants in the development of GIS, on the faculty (and still teaching a full course load). And while finances are a factor, I am fortunate that I'm in a position that I could do this option relatively cheaply without  that much in the way of loans.

Sorry for the rambling post just hoping for some guidance.