Adjusting the altitude levers is an integral part of the polar alignment process and can be done safely (and should be done) with the telescope attached to the saddle. Adjustments to the altitude/elevation should end with an upwards movement.
If you find that the adjustment levers are giving too much resistance, apply some grease. Unless you have an scope which is too heavy for your mount, they should be relatively easy to adjust. If necessary you can gently lift the front of your scope to relieve some of the downward force when making altitude adjustments in an upwards direction.
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This is no longer a problem for me now as I use an adaptor plate on a pier, the centre bolt is done up tight but because of moly grease between the eq6 and the plate plus between the plate and washer, azimuth adjustments are now silky smooth
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I highly recommend one of these plates -- you can purchase a pier extension which will work with any Celestron/Skywatcher EQ5/EQ6 mount for around $90. The supplied plate makes azimuth adjustments much easier and allows for more precise movement.
When running the polar alignment routine, try using a star to the North. I normally PA on Arcturus or Regulus, depending on what time it is.
You could also check your tripod levelling -- often the bubble level supplied on the mount is not truly level. I recommend using a digital level, Stanley make one which beeps when it is at 90 degrees...useful when you're busy adjusting the tripod legs!
I have the replacement bolts astro developments. But the altitude motion itself is very stiff if I release both bolts and try to move by hand...certainly no scope for precision 
