I see. So you want to prevent the reader from taking the video full screen? I don't believe that is possible any more than you can prevent the reader from changing font size. Apple is keen on its customers being able to adjust things to their liking.
That being the case, you'll want to use video that will scale well on the iPad. My example video looks great at full screen because it began life as 1080p. I think that you'll find that 720p video also does quite well on the iPad. Search on "optimizing video for iPad" for some very good info on how to do this. Of course, this all assumes that you have control over the clips that you will be using.
If you don't have control, perhaps a little social engineering in the title or comments will help. For example, using old video clips from the Internet Archive can be a challenge in this regard. Advise the reader that, for best results, to let the video play in place.
Even if you're not the creator of the video, you may be able to find a version that will be better than others. For example, this 1946 video on How to Study (http://archive.org/details/0261_How_to_Study_E00470_00_39_40_00) can be downloaded as MPEG4 (640x480 55.1 MB *.mp4) or h.264 (640x480 208.9 MB *,m4v). Opening thse two videos in QuickTime X Player reveals that the primary difference between them is the file size and that is caused by the bitrate. The H264 version is 3.15 MB/second whereas the MPEG-4 version is .832 MB/s, much lower.
Time to experiment. Dragging each of these two versions of the same film (original was probably 16mm) into an IBA 2 project, we find that both scale to full screen reasonably well. However, the higher bitrate H.264 version looks ever so slightly better. So even a 640x480 movie can look good in your IBA project if it has a decent bitrate.
So what did IBA's optimizer do to these two videos? We can deconstruct the project to find out. Here's how. First export to a standard *.ibooks file. Next, duplicate the file and change the suffix from *.ibooks to *.zip. Then, use a utility such as the free Stuffit Expander to unpack this ZIP file. You should wind up with a folder. Open that folder and look ito the subfolder named OPS, then assets, then media. There you'll find all of your videos. We can now examine our two videos to understand how they may have been changed by IBAs optimizer.
Right off, we see that they are now both *,.m4v files which is Apple's special container for H.264/AAC video. The original MPEG-4 file was in an *.mp4 container but was also using the H.264/AAC CODECs. No real change there. Opening them in QuickTime X Player, we see that they are both still 640x480 and have the same frame rate. No change there. The only substantial differences are with the bitrates and, consequently the file sizes, so lets document those:
Original *.mp4 file:---------- 55.1 MB----------0.823 MB/s
Original *.m4v file:----------208.9 MB---------3.15 MB/s
Optimized *.m4v file #1:-- 54.9 MB----------0.823 MB/s (this probably came from the *.mp4 file)
Optimized *.m4v file #2:-162.8 MB---------2.500 MB/s (this probably came from the original *.m4v file)
So, optimizing didn't change the .mp4 file much but it did reduce the bitrate and file size of the .m4v file. The optimizer had more to work with in the *.m4v case so that would explain why it looks slightly better.