How are you acquiring the ECG signal (with what type of amplfier and electrodes, etc.)? Is this animal or human research?
You almost certainly have some kind of AC coupling already (high-pass filter) - it just sounds like the time-constant is too long (filter setting is too low), leading to the wandering baseline (low frequency drift) due to movement artifact. Most ECG is acquired with a 0.5Hz to 40Hz bandpass filter (though 100Hz is preferred to minimize attenuation of high-frequency features when possible).
I'm not clear on why you don't want to simply apply a FIR or IIR high-pass filter to remove the baseline drift. It will slightly change the shape of the waveform, but it will not significantly affect the higher-frequency components that you are interested in measuring. The intervals that you are measuring should not be affected (each beat complex will be affected in the same way, so the interbeat intervals will be unaffected).
If you absolutely cannot tolerate any further filtering, then you either have to use a more sophisticated detrending (wavelet based) and/or peak detection (there are many algorithms out there - just do a search) or minimize the baseline drift by recording from different sites or using different electrode technology.
For ECG signal processing ideas, refer to this great article on ni.com: http://zone.ni.com/devzone/cda/tut/p/id/6349
Steve
National Instruments
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